library(multiMiR)
## Welcome to multiMiR.
## 
## multiMiR database URL has been set to the 
## default value: http://multimir.org/
## 
## Database Version: 2.3.0  Updated: 2020-04-15
library(clusterProfiler)
## 
## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
## 
## Please cite:
## 
## S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang, Q Wang, B Liu, R Wang,
## W Xie, T Wu, L Xie, G Yu. Using clusterProfiler to characterize
## multiomics data. Nature Protocols. 2024, doi:10.1038/s41596-024-01020-z
## 
## Attaching package: 'clusterProfiler'
## The following object is masked from 'package:multiMiR':
## 
##     select
## The following object is masked from 'package:stats':
## 
##     filter
library(org.Hs.eg.db)
## Loading required package: AnnotationDbi
## Loading required package: stats4
## Loading required package: BiocGenerics
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
##     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
##     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
##     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
##     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
##     tapply, union, unique, unsplit, which.max, which.min
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## Loading required package: IRanges
## Loading required package: S4Vectors
## 
## Attaching package: 'S4Vectors'
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##     rename
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##     findMatches
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##     expand.grid, I, unname
## 
## Attaching package: 'IRanges'
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##     slice
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##     windows
## 
## Attaching package: 'AnnotationDbi'
## The following object is masked from 'package:clusterProfiler':
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##     select
## 
library(stringr)
library(ggplot2)

The results here are deprecated in favor of MOFA variables selected using thres_L.

0. Loading of Results

A. List of all Gene names in the dataset

gene.names = readRDS("data/derived/unique_gene_names.rds")

B. Selected Features

results.mofa = readRDS("data/sel_features/results_mofa_top_5_percent.rds")
sel.features = results.mofa
sel.features
## $`1f`
## $`1f`$Factor1
## hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1193   hsa-mir-1197    hsa-mir-136 
##     -0.7629508     -0.7462546     -0.6264293     -0.8177493     -0.6225595 
##    hsa-mir-154    hsa-mir-323   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2 
##     -0.6243017     -0.7085735     -0.7171871     -0.9023781     -0.6506600 
##    hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2    hsa-mir-377    hsa-mir-380 
##     -0.6299468     -0.6462057     -0.7213440     -0.6137607     -0.7333177 
##    hsa-mir-382    hsa-mir-409    hsa-mir-410    hsa-mir-411    hsa-mir-431 
##     -0.6338445     -0.6219059     -0.6434716     -0.6958073     -0.6248299 
##    hsa-mir-432    hsa-mir-433    hsa-mir-485   hsa-mir-487a   hsa-mir-487b 
##     -0.6426433     -0.6436876     -0.6906152     -0.7452065     -0.6615326 
##    hsa-mir-494    hsa-mir-496    hsa-mir-539    hsa-mir-541    hsa-mir-543 
##     -0.6393844     -0.6347435     -0.6248115     -0.6876863     -0.6419155 
##    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668    hsa-mir-770 
##     -0.7051487     -0.7722097     -0.6770739     -0.8606763     -0.7888620 
##    hsa-mir-889 
##     -0.6473752 
## 
## 
## $`2f`
## $`2f`$Factor1
##   hsa-mir-1258   hsa-mir-135b    hsa-mir-506    hsa-mir-507    hsa-mir-508 
##     -0.2733195      0.2678525     -0.3185482     -0.2603344     -0.2774065 
##  hsa-mir-509-1  hsa-mir-509-2  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 
##     -0.2576410     -0.2573185     -0.2687342     -0.3650144     -0.3297462 
## hsa-mir-513a-2   hsa-mir-513b   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2 
##     -0.3227300     -0.3234853     -0.2877525     -0.3280582     -0.3258505 
##  hsa-mir-514-3    hsa-mir-605     STMN1.R2Gn    CTNNA1.R2Gn      G6PD.RPPA 
##     -0.3244563     -0.2620651      0.2568932     -0.2694667     -0.4501249 
##    IGFBP2.RPPA     RBM15.RPPA       ATM.RPPA     BRCA2.RPPA      FASN.RPPA 
##      0.3018783      0.7999696      0.3250985     -0.2550553      1.0536463 
##    INPP4B.RPPA      TSC1.RPPA      TTF1.RPPA       VHL.RPPA     PRDX1.RPPA 
##     -0.4189671      0.4269544     -0.3765308     -0.5905985     -0.5384414 
##      XBP1.RPPA     GAPDH.RPPA      MSH6.RPPA      TFRC.RPPA      MSH2.RPPA 
##     -0.3626753      0.2545084      0.7180545      0.4532162      0.2702868 
##     PREX1.RPPA 
##     -0.4629907 
## 
## $`2f`$Factor2
## hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1193   hsa-mir-1197    hsa-mir-127 
##     -0.8148004     -0.7998948     -0.6412522     -0.8151468     -0.6292322 
##    hsa-mir-136    hsa-mir-154    hsa-mir-323   hsa-mir-323b  hsa-mir-329-1 
##     -0.6456195     -0.6491630     -0.7357216     -0.7650560     -0.9230492 
##  hsa-mir-329-2    hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2    hsa-mir-380 
##     -0.6390089     -0.6397646     -0.6545057     -0.7125216     -0.7394387 
##    hsa-mir-382    hsa-mir-409    hsa-mir-410    hsa-mir-411    hsa-mir-431 
##     -0.6500180     -0.6377656     -0.6699741     -0.7572727     -0.6241728 
##    hsa-mir-432    hsa-mir-433    hsa-mir-485   hsa-mir-487a   hsa-mir-487b 
##     -0.6549299     -0.6954934     -0.7505666     -0.7678460     -0.6853095 
##    hsa-mir-494    hsa-mir-496    hsa-mir-539    hsa-mir-541    hsa-mir-543 
##     -0.6570549     -0.6631960     -0.6498181     -0.6976724     -0.7016385 
##    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668    hsa-mir-770 
##     -0.7417666     -0.7694766     -0.6560661     -0.9011633     -0.7715128 
##    hsa-mir-889 
##     -0.6736458 
## 
## 
## $`3f`
## $`3f`$Factor1
## hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1193   hsa-mir-1197    hsa-mir-136 
##     -0.7649038     -0.7472290     -0.6257883     -0.8151400     -0.6246587 
##    hsa-mir-154    hsa-mir-323   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2 
##     -0.6272125     -0.7104303     -0.7207944     -0.9035395     -0.6551830 
##    hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2    hsa-mir-377    hsa-mir-380 
##     -0.6311082     -0.6467226     -0.7206759     -0.6144270     -0.7321005 
##    hsa-mir-382    hsa-mir-409    hsa-mir-410    hsa-mir-411    hsa-mir-431 
##     -0.6356706     -0.6233494     -0.6455569     -0.7016670     -0.6259743 
##    hsa-mir-432    hsa-mir-433    hsa-mir-485   hsa-mir-487a   hsa-mir-487b 
##     -0.6441280     -0.6460453     -0.6992923     -0.7463014     -0.6639803 
##    hsa-mir-494    hsa-mir-496    hsa-mir-539    hsa-mir-541    hsa-mir-543 
##     -0.6413019     -0.6368647     -0.6271768     -0.6866341     -0.6493149 
##    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668    hsa-mir-770 
##     -0.7073773     -0.7716958     -0.6887911     -0.8602373     -0.7952202 
##    hsa-mir-889 
##     -0.6500319 
## 
## $`3f`$Factor2
##   hsa-mir-1258   hsa-mir-135b    hsa-mir-139    hsa-mir-182    hsa-mir-183 
##     -0.4302970      0.2926786      0.3497486      0.2766422      0.2841530 
## hsa-mir-196a-1   hsa-mir-196b   hsa-mir-2114  hsa-mir-218-1  hsa-mir-218-2 
##      0.2896094      0.2862292     -0.3140284      0.2630450      0.3165759 
##   hsa-mir-3166   hsa-mir-3170   hsa-mir-3655   hsa-mir-3923    hsa-mir-485 
##      0.3280705      0.2912757     -0.3138855      0.2732425     -0.2914957 
##    hsa-mir-506    hsa-mir-507    hsa-mir-508  hsa-mir-509-1  hsa-mir-509-2 
##     -0.8235410     -0.8798237     -0.7841521     -0.7517999     -0.7475504 
##  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2   hsa-mir-513b 
##     -0.7555578     -0.9424875     -0.8275008     -0.9246400     -0.7336730 
##   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3   hsa-mir-514b 
##     -0.7541221     -0.8465889     -0.8511083     -0.8518621     -0.7302340 
##    hsa-mir-543    hsa-mir-615    hsa-mir-887     RBM15.RPPA      TSC1.RPPA 
##     -0.2690902      0.2833678      0.2814917      0.3592209      0.3981680 
##       VHL.RPPA 
##     -0.4164379 
## 
## $`3f`$Factor3
##    ERBB3.R2Gn EIF4EBP1.R2Gn    RAD51.R2Gn    GATA3.R2Gn   EIF4G1.R2Gn 
##     0.1783920    -0.1062276    -0.1104642    -0.1367058     0.2075635 
##    BIRC2.R2Gn    XRCC5.R2Gn     ADAR.R2Gn    BRCA2.R2Gn     CDH3.R2Gn 
##     0.1173165     0.1651795     0.1023714    -0.1202103    -0.1410888 
##    PDCD4.R2Gn     PTK2.R2Gn    PRRT2.R2Gn     CDK1.R2Gn    MS4A1.R2Gn 
##     0.1247360     0.1060514    -0.1404151    -0.1130961    -0.1204415 
##      LCK.R2Gn   CTNNA1.R2Gn       AR.R2Gn     TP63.R2Gn    GAPDH.R2Gn 
##    -0.1014332     0.1033851    -0.1052590    -0.1298156    -0.1045300 
##    CCNB1.R2Gn     KRT5.R2Gn     MYH9.R2Gn    FOXM1.R2Gn    YWHAB.R2Gn 
##    -0.1019111    -0.1134706     0.1640659    -0.1226586     0.1995448 
##     EZH2.R2Gn    RAB25.R2Gn     TFRC.R2Gn    CCNE2.R2Gn   ERRFI1.R2Gn 
##    -0.1077541    -0.1242253     0.1097051    -0.1034474     0.1602822 
##    PARP1.R2Gn    NAPSA.R2Gn     TFF1.R2Gn    MACC1.R2Gn     CHGA.R2Gn 
##     0.1888216    -0.1226086    -0.1282434    -0.1100881    -0.1047388 
##   KCNJ13.R2Gn 
##    -0.1289491 
## 
## 
## $`5f`
## $`5f`$Factor1
## hsa-mir-101-2  hsa-mir-146a   hsa-mir-150   hsa-mir-362     FASN.R2Gn 
##    -0.1386771    -0.1437377    -0.1506117    -0.1510695     0.1568808 
##    PRKCA.R2Gn     ANLN.R2Gn    STMN1.R2Gn     CDK1.R2Gn   CTNNA1.R2Gn 
##    -0.1520284     0.1453249     0.1986635     0.2107954    -0.1736660 
##     TYMS.R2Gn    CCNB1.R2Gn    FOXM1.R2Gn    YWHAB.R2Gn     G6PD.RPPA 
##     0.1766839     0.1914999     0.1679303    -0.1412905    -0.2784869 
##   IGFBP2.RPPA    RBM15.RPPA    GATA3.RPPA      ATM.RPPA    BRCA2.RPPA 
##     0.2231534     0.5884744    -0.3249034     0.2610943    -0.2230770 
##     FASN.RPPA   INPP4B.RPPA   ACVRL1.RPPA     TSC1.RPPA     TTF1.RPPA 
##     0.9309107    -0.3657546    -0.1384248     0.2800193    -0.2885557 
##     CDK1.RPPA     IRS1.RPPA      VHL.RPPA    PRDX1.RPPA     XBP1.RPPA 
##    -0.2259187    -0.1483742    -0.4192049    -0.4660874    -0.3349707 
##    GAPDH.RPPA     MSH6.RPPA    MYH11.RPPA     TFRC.RPPA     MSH2.RPPA 
##     0.3190805     0.6825490    -0.2656290     0.4747938     0.2681282 
##    PREX1.RPPA 
##    -0.3944828 
## 
## $`5f`$Factor2
## hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1193   hsa-mir-1197    hsa-mir-127 
##     -0.7585875     -0.7579153     -0.6106161     -0.8063115     -0.6067963 
##    hsa-mir-136    hsa-mir-154    hsa-mir-323   hsa-mir-323b  hsa-mir-329-1 
##     -0.6274709     -0.6174549     -0.7101262     -0.7288977     -0.9205374 
##  hsa-mir-329-2    hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2    hsa-mir-380 
##     -0.6773367     -0.6270633     -0.6579611     -0.6664014     -0.7120968 
##    hsa-mir-382    hsa-mir-409    hsa-mir-410    hsa-mir-411    hsa-mir-431 
##     -0.6251879     -0.6185533     -0.6469681     -0.6913067     -0.6398707 
##    hsa-mir-432    hsa-mir-433    hsa-mir-485   hsa-mir-487a   hsa-mir-487b 
##     -0.6475080     -0.6672985     -0.6710682     -0.7257411     -0.6719176 
##    hsa-mir-494    hsa-mir-496    hsa-mir-539    hsa-mir-541    hsa-mir-543 
##     -0.6089900     -0.6448792     -0.6358414     -0.6879424     -0.6286093 
##    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668    hsa-mir-770 
##     -0.6985868     -0.7680615     -0.7129604     -0.8759764     -0.8024955 
##    hsa-mir-889 
##     -0.6434183 
## 
## $`5f`$Factor3
## hsa-mir-1185-1   hsa-mir-1258   hsa-mir-135b    hsa-mir-139    hsa-mir-182 
##     -0.2693898     -0.3686553      0.2490502      0.3217925      0.2398068 
##    hsa-mir-183   hsa-mir-196b   hsa-mir-2114  hsa-mir-218-2   hsa-mir-3166 
##      0.2430847      0.2401641     -0.2789480      0.2598653      0.2902097 
##   hsa-mir-3170   hsa-mir-3655 hsa-mir-376a-2   hsa-mir-3923    hsa-mir-411 
##      0.2486504     -0.2836783     -0.2643668      0.2339307     -0.2921805 
##    hsa-mir-485   hsa-mir-487a    hsa-mir-494    hsa-mir-506    hsa-mir-507 
##     -0.3417393     -0.2342592     -0.2366182     -0.7359853     -0.8076562 
##    hsa-mir-508  hsa-mir-509-1  hsa-mir-509-2  hsa-mir-509-3    hsa-mir-510 
##     -0.7308223     -0.7148668     -0.7105480     -0.7097014     -0.8157004 
## hsa-mir-513a-1 hsa-mir-513a-2   hsa-mir-513b   hsa-mir-513c  hsa-mir-514-1 
##     -0.7257079     -0.8095509     -0.6391351     -0.6802698     -0.7502505 
##  hsa-mir-514-2  hsa-mir-514-3   hsa-mir-514b    hsa-mir-543    hsa-mir-615 
##     -0.7560365     -0.7577167     -0.6915826     -0.3114163      0.2358871 
##    hsa-mir-668 
##     -0.2524937 
## 
## $`5f`$Factor4
##    hsa-mir-100    hsa-mir-10a   hsa-mir-1226   hsa-mir-1249   hsa-mir-1258 
##     0.09092840     0.10430926    -0.09205737     0.09425247    -0.08713839 
##   hsa-mir-133b    hsa-mir-136    hsa-mir-139    hsa-mir-195    hsa-mir-27a 
##     0.08922739     0.09398186     0.11903941     0.12217991     0.08887515 
##    hsa-mir-29c   hsa-mir-301a   hsa-mir-3200    hsa-mir-338    hsa-mir-421 
##     0.11238619    -0.09142878    -0.11185583     0.08631410    -0.08392455 
##    hsa-mir-424    hsa-mir-431 hsa-mir-450a-1 hsa-mir-450a-2    hsa-mir-483 
##     0.10314917    -0.09069324     0.09329516     0.09112324    -0.15440452 
##    hsa-mir-497   hsa-mir-518c    hsa-mir-937    hsa-mir-940     hsa-mir-95 
##     0.10858906     0.10784148    -0.08603576    -0.09177980     0.10658063 
##      G6PD.RPPA      PTEN.RPPA     PEA15.RPPA      EGFR.RPPA      FASN.RPPA 
##    -0.14609040     0.09169299     0.19406851     0.12075721     0.08668146 
##      CDK1.RPPA      IRS1.RPPA       VHL.RPPA      XBP1.RPPA      MSH2.RPPA 
##    -0.09550971     0.09575202    -0.11997307    -0.12221368    -0.09643250 
##     PREX1.RPPA 
##    -0.13058908 
## 
## $`5f`$Factor5
## MAPK14.R2Gn  ERBB3.R2Gn   AKT2.R2Gn  RAD51.R2Gn  GATA3.R2Gn EIF4G1.R2Gn 
##  0.10707272  0.15159766  0.10220584 -0.08782818 -0.10681824  0.17254253 
##  MAPK1.R2Gn  BIRC2.R2Gn  XRCC5.R2Gn  BRCA2.R2Gn   LCN2.R2Gn   CDH3.R2Gn 
##  0.09778135  0.12000357  0.16537122 -0.10494009 -0.09685022 -0.13429995 
##  PDCD4.R2Gn   PTK2.R2Gn  PRRT2.R2Gn  MS4A1.R2Gn    LCK.R2Gn     AR.R2Gn 
##  0.10885774  0.10031383 -0.13514514 -0.11782608 -0.10713095 -0.11004834 
##   TP63.R2Gn  GAPDH.R2Gn   NRG1.R2Gn   KRT5.R2Gn   MYH9.R2Gn  FOXM1.R2Gn 
## -0.11901601 -0.08857987 -0.09126953 -0.10776611  0.14014417 -0.09110170 
##  YWHAB.R2Gn  RAB25.R2Gn  ERCC1.R2Gn    BID.R2Gn   TFRC.R2Gn ERRFI1.R2Gn 
##  0.16302468 -0.11733783 -0.08760359 -0.09582430  0.10668702  0.13746126 
##  PARP1.R2Gn  NAPSA.R2Gn   TFF1.R2Gn  MACC1.R2Gn   CHGA.R2Gn KCNJ13.R2Gn 
##  0.18604508 -0.11670010 -0.11688121 -0.11090805 -0.09129306 -0.12196921 
## 
## 
## $`10f`
## $`10f`$Factor1
##   hsa-mir-146a    hsa-mir-150 hsa-mir-196a-1    hsa-mir-362    hsa-mir-653 
##      0.2439511      0.2176340     -0.1894599      0.2013512      0.2167146 
##      FASN.R2Gn     PRKCA.R2Gn     STMN1.R2Gn      CDK1.R2Gn    CTNNA1.R2Gn 
##     -0.1960203      0.1897229     -0.2373242     -0.2289052      0.2068288 
##      TYMS.R2Gn      MSH6.R2Gn     CCNB1.R2Gn     PREX1.R2Gn      G6PD.RPPA 
##     -0.1729913     -0.1780294     -0.2314913      0.1735357      0.4649610 
##    IGFBP2.RPPA      ASNS.RPPA     RBM15.RPPA     GATA3.RPPA     PEA15.RPPA 
##     -0.2495660      0.1845150     -0.7031606      0.4185162     -0.1961371 
##       ATM.RPPA     BRCA2.RPPA      FASN.RPPA    INPP4B.RPPA      TSC1.RPPA 
##     -0.2976696      0.2778099     -1.1854465      0.4445420     -0.3088216 
##      TTF1.RPPA      CDK1.RPPA       VHL.RPPA     PRDX1.RPPA      XBP1.RPPA 
##      0.3018635      0.3171725      0.5434133      0.5653009      0.3994834 
##     GAPDH.RPPA      MSH6.RPPA     MYH11.RPPA      TFRC.RPPA      MSH2.RPPA 
##     -0.5204806     -0.8080000      0.2798145     -0.4650862     -0.2984680 
##     PREX1.RPPA 
##      0.5079902 
## 
## $`10f`$Factor2
## hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1193   hsa-mir-1197    hsa-mir-127 
##     -0.7757787     -0.7684686     -0.6118972     -0.8106640     -0.6143032 
##    hsa-mir-136    hsa-mir-154    hsa-mir-323   hsa-mir-323b  hsa-mir-329-1 
##     -0.6320459     -0.6310229     -0.7222756     -0.7419769     -0.9263064 
##  hsa-mir-329-2    hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2    hsa-mir-380 
##     -0.6799496     -0.6314871     -0.6638160     -0.6738463     -0.7232468 
##    hsa-mir-382    hsa-mir-409    hsa-mir-410    hsa-mir-411    hsa-mir-431 
##     -0.6325155     -0.6230285     -0.6622328     -0.7261397     -0.6425268 
##    hsa-mir-432    hsa-mir-433    hsa-mir-485   hsa-mir-487a   hsa-mir-487b 
##     -0.6511705     -0.6874613     -0.6997358     -0.7420009     -0.6732689 
##    hsa-mir-494    hsa-mir-496    hsa-mir-539    hsa-mir-541    hsa-mir-543 
##     -0.6323493     -0.6429590     -0.6406990     -0.6928630     -0.6504994 
##    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668    hsa-mir-770 
##     -0.7303706     -0.7603929     -0.6939368     -0.8925683     -0.7861210 
##    hsa-mir-889 
##     -0.6554383 
## 
## $`10f`$Factor3
## hsa-let-7a-1 hsa-let-7a-2 hsa-let-7a-3 hsa-let-7f-1 hsa-let-7f-2 hsa-mir-1229 
##  -0.05801089  -0.05686941  -0.05791394  -0.06823632  -0.06271406   0.06294886 
##  hsa-mir-214  hsa-mir-23a hsa-mir-3200    G6PD.RPPA  IGFBP2.RPPA   RBM15.RPPA 
##  -0.05434345  -0.05925805   0.05633602   0.35292467   0.22359502  -0.30910647 
##    PTEN.RPPA   GATA3.RPPA   PEA15.RPPA     ATM.RPPA   BRCA2.RPPA    EGFR.RPPA 
##  -0.45634142   0.14007989  -0.22443563  -0.25097775   0.11915235  -0.15185097 
##    FASN.RPPA  INPP4B.RPPA    PCNA.RPPA  ACVRL1.RPPA    TSC1.RPPA   PDCD4.RPPA 
##   0.08621731   0.20455523   0.09210050   0.14015430  -0.18266179  -0.41097477 
##    CDK1.RPPA   XRCC1.RPPA    IRS1.RPPA     VHL.RPPA      AR.RPPA   PRDX1.RPPA 
##   0.16809660   0.08300330  -0.12852126   0.22653894  -0.07744230   0.25950259 
##    XBP1.RPPA     NF2.RPPA   ERCC1.RPPA    TFRC.RPPA    MSH2.RPPA   PREX1.RPPA 
##   0.24001938  -0.10919836  -0.14765766  -0.17888249   0.12918670   0.21356429 
## 
## $`10f`$Factor4
##   hsa-mir-1226   hsa-mir-1249   hsa-mir-1258   hsa-mir-135b    hsa-mir-139 
##      0.2013880      0.2013092     -0.3447852      0.2185706      0.2925311 
##    hsa-mir-182    hsa-mir-183    hsa-mir-184   hsa-mir-196b   hsa-mir-2114 
##      0.2095041      0.2128228     -0.2045339      0.2097269     -0.2516953 
##  hsa-mir-218-2   hsa-mir-3166   hsa-mir-3170   hsa-mir-3655 hsa-mir-376a-2 
##      0.2043498      0.2622004      0.2178932     -0.2656059     -0.2118430 
##   hsa-mir-3923    hsa-mir-485    hsa-mir-506    hsa-mir-507    hsa-mir-508 
##      0.2342099     -0.2529788     -0.6782678     -0.7587051     -0.6876708 
##  hsa-mir-509-1  hsa-mir-509-2  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 
##     -0.6887159     -0.6844518     -0.6827294     -0.8044964     -0.6867524 
## hsa-mir-513a-2   hsa-mir-513b   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2 
##     -0.7446260     -0.6228126     -0.6547784     -0.6779802     -0.6837980 
##  hsa-mir-514-3   hsa-mir-514b    hsa-mir-543    hsa-mir-582    hsa-mir-615 
##     -0.6835320     -0.6983735     -0.2354951      0.2105771      0.2115752 
##    hsa-mir-92b 
##      0.2082682 
## 
## $`10f`$Factor5
##  hsa-mir-1224  hsa-mir-125a   hsa-mir-202   hsa-mir-29c  hsa-mir-301a 
##   -0.07757617   -0.07368264   -0.07087204   -0.09390491    0.07492819 
##   hsa-mir-766 EIF4EBP1.R2Gn     NRAS.R2Gn    MAPK9.R2Gn     EGFR.R2Gn 
##   -0.08679421    0.06772254    0.07322794   -0.10262868   -0.08042480 
##   ACVRL1.R2Gn   PECAM1.R2Gn   RAB11A.R2Gn    EEF2K.R2Gn    RAD50.R2Gn 
##    0.07327735    0.07790451   -0.10008703   -0.09475668   -0.11121136 
##     TYMS.R2Gn     XIAP.R2Gn    PARP1.R2Gn    ANXA7.R2Gn   IGFBP2.RPPA 
##    0.07976948   -0.07202139    0.08127678   -0.08679935    0.14329337 
##     ASNS.RPPA    RBM15.RPPA     PTEN.RPPA      ATM.RPPA    BRCA2.RPPA 
##    0.12955621    0.14449525   -0.12278367    0.09622584    0.06847188 
##     EGFR.RPPA   ACVRL1.RPPA     TSC1.RPPA     TTF1.RPPA     CDK1.RPPA 
##   -0.17544550    0.08678960    0.15464054   -0.07050533    0.07800888 
##     IRS1.RPPA    GAPDH.RPPA     MSH6.RPPA     PDK1.RPPA    ERCC1.RPPA 
##   -0.06691432   -0.16643153    0.08321948   -0.06834891   -0.19305989 
##     TFRC.RPPA 
##    0.07729538 
## 
## $`10f`$Factor6
## AKT1S1.R2Gn    SRC.R2Gn  MAPK1.R2Gn   VASP.R2Gn  ITGA2.R2Gn  YWHAE.R2Gn 
## -0.06530473 -0.06137238  0.07006741 -0.07346763  0.06533720 -0.09718410 
##   TSC1.R2Gn   ANLN.R2Gn  PDCD4.R2Gn  GSK3A.R2Gn RAB11B.R2Gn  KEAP1.R2Gn 
## -0.06199414  0.08852450 -0.06254116 -0.08128472 -0.07358222 -0.06263774 
##  XRCC1.R2Gn   PDK1.R2Gn MAP2K1.R2Gn  FOXM1.R2Gn  ERCC1.R2Gn   G6PD.RPPA 
## -0.10397790  0.06057473  0.09030174  0.07717057 -0.07147568  0.14335443 
##   ASNS.RPPA  RBM15.RPPA   PTEN.RPPA  GATA3.RPPA  PEA15.RPPA    ATM.RPPA 
##  0.19428484 -0.28288889 -0.06120672 -0.18584156  0.13874172 -0.11923894 
##   EGFR.RPPA  PDCD4.RPPA   IRS1.RPPA    VHL.RPPA   XBP1.RPPA  GAPDH.RPPA 
##  0.16687511 -0.08123798  0.12930401 -0.06729201 -0.09220541  0.16526712 
##   MSH6.RPPA  MYH11.RPPA    NF2.RPPA   PDK1.RPPA   TFRC.RPPA  PREX1.RPPA 
##  0.07068952 -0.13618457 -0.11466402  0.06047169  0.09673942 -0.20894785 
## 
## $`10f`$Factor7
## hsa-mir-3074  MAPK14.R2Gn   ERBB3.R2Gn    AKT3.R2Gn    CDH2.R2Gn   RAD51.R2Gn 
##   0.07930424  -0.09080391  -0.09733605  -0.07428569  -0.08697511   0.07849700 
##   BECN1.R2Gn   BIRC2.R2Gn   ITGA2.R2Gn    ADAR.R2Gn   BRCA2.R2Gn    PCNA.R2Gn 
##  -0.09878736  -0.06614775  -0.07324430  -0.12430753   0.06620272   0.12726545 
##  CTNNB1.R2Gn    ANLN.R2Gn    SHC1.R2Gn   STMN1.R2Gn   ACACB.R2Gn    CDK1.R2Gn 
##  -0.07196339   0.22669883  -0.09211306   0.22997268  -0.07505351   0.20357363 
##    E2F1.R2Gn   XRCC1.R2Gn    TYMS.R2Gn   CCNB1.R2Gn  TUBA1B.R2Gn  NOTCH3.R2Gn 
##   0.11854476   0.07422303   0.13062122   0.21480298   0.10910680   0.07228020 
##   FOXM1.R2Gn    EZH2.R2Gn   CCNE2.R2Gn  ERRFI1.R2Gn   PARP1.R2Gn   RPTOR.R2Gn 
##   0.18389165   0.10342199   0.09657363  -0.08004816  -0.10325056  -0.07926491 
##  CDKN2A.R2Gn   PEA15.RPPA  INPP4B.RPPA    PCNA.RPPA  ACVRL1.RPPA     NF2.RPPA 
##   0.09057715  -0.06904783  -0.06605250   0.07415823  -0.06682102  -0.07900642 
## 
## $`10f`$Factor8
##    ERBB3.R2Gn EIF4EBP1.R2Gn     AKT2.R2Gn    CLDN7.R2Gn     ESR1.R2Gn 
##   -0.08224300    0.07072022   -0.08641771    0.08638426    0.07944772 
##    GATA3.R2Gn   EIF4G1.R2Gn      AXL.R2Gn    MAPK1.R2Gn    BIRC2.R2Gn 
##    0.07285401   -0.13453801    0.07267915   -0.08100040   -0.07640026 
##    XRCC5.R2Gn     LCN2.R2Gn     CDH3.R2Gn    PDCD4.R2Gn     PTK2.R2Gn 
##   -0.11221777    0.07404122    0.10597123   -0.08704497   -0.07893465 
##    PRRT2.R2Gn    MS4A1.R2Gn      LCK.R2Gn   CTNNA1.R2Gn     TP63.R2Gn 
##    0.09576759    0.09444701    0.09407651   -0.07267374    0.09729126 
##     NRG1.R2Gn     KRT5.R2Gn     MYH9.R2Gn    YWHAB.R2Gn    RAB25.R2Gn 
##    0.07899287    0.09340290   -0.08806494   -0.13172348    0.09895545 
##      BID.R2Gn     TFRC.R2Gn   ERRFI1.R2Gn    PARP1.R2Gn    CASP9.R2Gn 
##    0.08035962   -0.08377423   -0.07313473   -0.11041104    0.07580432 
##    NAPSA.R2Gn      SYK.R2Gn     TFF1.R2Gn    MACC1.R2Gn     CHGA.R2Gn 
##    0.09265782    0.09534506    0.09923044    0.08408040    0.08330778 
##   KCNJ13.R2Gn 
##    0.09958442 
## 
## $`10f`$Factor9
##   hsa-let-7a-1   hsa-let-7a-3     hsa-let-7e   hsa-let-7f-1   hsa-let-7f-2 
##    -0.07351197    -0.07362586    -0.10535952    -0.09033088    -0.09345894 
##    hsa-mir-10a   hsa-mir-1197   hsa-mir-1249  hsa-mir-128-2    hsa-mir-134 
##     0.08653057    -0.07932135     0.07170332    -0.07785700     0.07713903 
##    hsa-mir-142   hsa-mir-146b    hsa-mir-195    hsa-mir-197    hsa-mir-205 
##     0.11448278     0.07687828     0.08075973     0.07460224     0.09066726 
##   hsa-mir-2110    hsa-mir-29c   hsa-mir-3200    hsa-mir-421    hsa-mir-483 
##    -0.08394032     0.07649425    -0.08255380    -0.10029192    -0.10543139 
##   hsa-mir-514b hsa-mir-516a-1 hsa-mir-516a-2 hsa-mir-516b-1   hsa-mir-517a 
##     0.09014382     0.08803593     0.09923389     0.08826557     0.10131671 
##   hsa-mir-518b   hsa-mir-518c   hsa-mir-518f hsa-mir-519a-2    hsa-mir-525 
##     0.09169916     0.10279340     0.11103735     0.08638884     0.07590113 
##   hsa-mir-526b    hsa-mir-627    hsa-mir-655    hsa-mir-765    hsa-mir-877 
##     0.07759569     0.09695566     0.08207855    -0.09110382    -0.08039207 
##     hsa-mir-98 
##    -0.07509896 
## 
## $`10f`$Factor10
##   hsa-mir-106a    hsa-mir-107    hsa-mir-10b   hsa-mir-1226   hsa-mir-125a 
##     0.08792105     0.05218595    -0.05511979    -0.06467026    -0.05393226 
## hsa-mir-125b-1   hsa-mir-1307    hsa-mir-144   hsa-mir-16-1   hsa-mir-16-2 
##    -0.04745908    -0.04976137     0.06520889     0.05097669     0.04599367 
##    hsa-mir-185    hsa-mir-18a    hsa-mir-19a  hsa-mir-19b-2    hsa-mir-20a 
##     0.05757672     0.08705410     0.04928057     0.05379727     0.05476943 
##    hsa-mir-20b    hsa-mir-223    hsa-mir-23a   hsa-mir-301a    hsa-mir-30e 
##     0.05628907     0.05646559    -0.06209031    -0.05890957    -0.05636798 
##    hsa-mir-328    hsa-mir-363   hsa-mir-374b    hsa-mir-377    hsa-mir-451 
##    -0.05122608     0.09423997     0.05124469     0.04763857     0.06474881 
##    hsa-mir-486    hsa-mir-510 hsa-mir-550a-1    hsa-mir-616    hsa-mir-652 
##     0.05457522     0.04980592     0.06231136    -0.04829336     0.05510786 
##    hsa-mir-660    hsa-mir-99b     BRCA2.RPPA      PCNA.RPPA      IRS1.RPPA 
##     0.04716566    -0.08297141     0.06675472     0.05366337     0.09403171 
##       NF2.RPPA 
##     0.06943242

1. Convert microRNA to genes

Also remove the ending “.R2Gn” and “.RPPA” from gene names.

split.by.omic = function(variable.list) {
  out.mRSG = variable.list[startsWith(variable.list, "hsa")]
  out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
  out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
  out = list("miRNASeqGene" = out.mRSG,
             "RNASeq2GeneNorm" = out.R2Gn,
             "RPPAArray" = out.RPPA)
  out
}
multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
  multiomics.list = split.by.omic(sel.features)
  # Convert miRNASeqGene to target GENE names
  # Skipped and returns an empty list instead of the list of select features,
  # or if microRNA features are explicitly dropped (drop.miRNA = T).
  # (Usually done when the features has only a few miRNA and unable to target any genes)
  if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
    if (!full.search) { # Search only among the 198 genes in ACC, recommended
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          target = gene.names,
                          table = table,
                          summary = T)
    mRSG.target.genes = unique(targets@data$target_symbol)
    } else { # Search the full dataset, not recommended. 
             # Use only if ACC gene search returns nothing or fails.
             # Genes not in the ACC genes need to be manually removed.
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          table = table,
                          summary = T)  
    mRSG.target.genes = unique(targets@data$target_symbol)
    }
    
  } else {
    mRSG.target.genes = list()
  }
  #Remove suffix for Pathway Analysis Compatibility
  R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
  
  RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
  
  #Join all cleaned-up genes are remove duplicates.
  out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes)
  out = as.character(unique(out1))
  out
}
geneNames <- list("Factor1of1"= multiomics.to.GENES(names(sel.features$`1f`$Factor1)),
                  
                  "Factor1of2"= multiomics.to.GENES(names(sel.features$`2f`$Factor1)),
                  "Factor2of2"= multiomics.to.GENES(names(sel.features$`2f`$Factor2)),
                  
                  "Factor1of3"= multiomics.to.GENES(names(sel.features$`3f`$Factor1)),
                  "Factor2of3"= multiomics.to.GENES(names(sel.features$`3f`$Factor2)),
                  "Factor3of3"= multiomics.to.GENES(names(sel.features$`3f`$Factor3)),
                  
                  "Factor1of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor1), drop.miRNA = T),
                  "Factor2of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor2)),
                  "Factor3of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor3)),
                  "Factor4of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor4)),
                  "Factor5of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor5)),
                  
                  "Factor1of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor1), drop.miRNA = T),
                  "Factor2of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor2)),
                  "Factor3of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor3), drop.miRNA = T),
                  "Factor4of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor4)),
                  "Factor5of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor5), drop.miRNA = T),
                  "Factor6of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor6)),
                  "Factor7of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor7), drop.miRNA = T),
                  "Factor8of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor8)),
                  "Factor9of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor9)),
                  "Factor10of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor10))
                  )
## Searching mirecords ...
## Searching mirtarbase ...
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geneNames
## $Factor1of1
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "PTEN"   "KRAS"   "NRAS"   "PTK2"   "ETS1"  
## [17] "CCND1"  "XIAP"   "STAT5A" "YAP1"   "ITGA2"  "MAPK1"  "ANLN"  
## 
## $Factor1of2
##  [1] "RB1"    "XIAP"   "ETS1"   "MAPK8"  "ARID1A" "BID"    "NCOA3"  "GAB2"  
##  [9] "STMN1"  "CTNNA1" "G6PD"   "IGFBP2" "RBM15"  "ATM"    "BRCA2"  "FASN"  
## [17] "INPP4B" "TSC1"   "TTF1"   "VHL"    "PRDX1"  "XBP1"   "GAPDH"  "MSH6"  
## [25] "TFRC"   "MSH2"   "PREX1" 
## 
## $Factor2of2
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "PTEN"   "KRAS"   "NRAS"   "PTK2"   "ETS1"  
## [17] "CCND1"  "XIAP"   "STAT5A" "YAP1"   "ITGA2"  "MAPK1"  "ANLN"  
## 
## $Factor1of3
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "PTEN"   "KRAS"   "NRAS"   "PTK2"   "ETS1"  
## [17] "CCND1"  "XIAP"   "STAT5A" "YAP1"   "ITGA2"  "MAPK1"  "ANLN"  
## 
## $Factor2of3
##  [1] "RB1"    "XIAP"   "ETS1"   "MAPK8"  "ARID1A" "BID"    "PTEN"   "KRAS"  
##  [9] "NRAS"   "PTK2"   "ATM"    "YWHAZ"  "CCND1"  "CDKN1A" "NCOA3"  "GAB2"  
## [17] "ITGA2"  "RBM15"  "TSC1"   "VHL"   
## 
## $Factor3of3
##  [1] "ERBB3"    "EIF4EBP1" "RAD51"    "GATA3"    "EIF4G1"   "BIRC2"   
##  [7] "XRCC5"    "ADAR"     "BRCA2"    "CDH3"     "PDCD4"    "PTK2"    
## [13] "PRRT2"    "CDK1"     "MS4A1"    "LCK"      "CTNNA1"   "AR"      
## [19] "TP63"     "GAPDH"    "CCNB1"    "KRT5"     "MYH9"     "FOXM1"   
## [25] "YWHAB"    "EZH2"     "RAB25"    "TFRC"     "CCNE2"    "ERRFI1"  
## [31] "PARP1"    "NAPSA"    "TFF1"     "MACC1"    "CHGA"     "KCNJ13"  
## 
## $Factor1of5
##  [1] "FASN"   "PRKCA"  "ANLN"   "STMN1"  "CDK1"   "CTNNA1" "TYMS"   "CCNB1" 
##  [9] "FOXM1"  "YWHAB"  "G6PD"   "IGFBP2" "RBM15"  "GATA3"  "ATM"    "BRCA2" 
## [17] "INPP4B" "ACVRL1" "TSC1"   "TTF1"   "IRS1"   "VHL"    "PRDX1"  "XBP1"  
## [25] "GAPDH"  "MSH6"   "MYH11"  "TFRC"   "MSH2"   "PREX1" 
## 
## $Factor2of5
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "PTEN"   "KRAS"   "NRAS"   "PTK2"   "ETS1"  
## [17] "CCND1"  "XIAP"   "STAT5A" "YAP1"   "ITGA2"  "MAPK1"  "ANLN"  
## 
## $Factor3of5
##  [1] "RB1"    "XIAP"   "ETS1"   "MAPK8"  "ARID1A" "BID"    "PTEN"   "KRAS"  
##  [9] "NRAS"   "PTK2"   "ATM"    "YWHAZ"  "CCND1"  "CDKN1A" "NCOA3"  "ITGA2" 
## [17] "GAB2"  
## 
## $Factor4of5
##  [1] "EGFR"     "MET"      "AKT1"     "BCL2L1"   "IGF1R"    "CASP3"   
##  [7] "CDH1"     "ATM"      "XIAP"     "SMAD4"    "MAPK8"    "TUBA1B"  
## [13] "RB1"      "NF2"      "E2F1"     "MYH9"     "MYC"      "YWHAZ"   
## [19] "CASP8"    "RAD51"    "NDRG1"    "ACVRL1"   "NCOA3"    "PARP1"   
## [25] "EIF4EBP1" "NRAS"     "CDKN1B"   "CTNNA1"   "MTOR"     "PRDX1"   
## [31] "SERPINE1" "PRKAA1"   "PXN"      "SRSF1"    "TFRC"     "YWHAB"   
## [37] "ERBB2"    "ADAR"     "JUN"      "NOTCH3"   "BCL2L11"  "TP53"    
## [43] "AKT2"     "XBP1"     "STAT3"    "EEF2"     "EIF4G1"   "GAPDH"   
## [49] "VASP"     "ARID1A"   "AKT1S1"   "RICTOR"   "PTCH1"    "FASN"    
## [55] "G6PD"     "PTEN"     "PEA15"    "CDK1"     "IRS1"     "VHL"     
## [61] "MSH2"     "PREX1"   
## 
## $Factor5of5
##  [1] "MAPK14" "ERBB3"  "AKT2"   "RAD51"  "GATA3"  "EIF4G1" "MAPK1"  "BIRC2" 
##  [9] "XRCC5"  "BRCA2"  "LCN2"   "CDH3"   "PDCD4"  "PTK2"   "PRRT2"  "MS4A1" 
## [17] "LCK"    "AR"     "TP63"   "GAPDH"  "NRG1"   "KRT5"   "MYH9"   "FOXM1" 
## [25] "YWHAB"  "RAB25"  "ERCC1"  "BID"    "TFRC"   "ERRFI1" "PARP1"  "NAPSA" 
## [33] "TFF1"   "MACC1"  "CHGA"   "KCNJ13"
## 
## $Factor1of10
##  [1] "FASN"   "PRKCA"  "STMN1"  "CDK1"   "CTNNA1" "TYMS"   "MSH6"   "CCNB1" 
##  [9] "PREX1"  "G6PD"   "IGFBP2" "ASNS"   "RBM15"  "GATA3"  "PEA15"  "ATM"   
## [17] "BRCA2"  "INPP4B" "TSC1"   "TTF1"   "VHL"    "PRDX1"  "XBP1"   "GAPDH" 
## [25] "MYH11"  "TFRC"   "MSH2"  
## 
## $Factor2of10
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "PTEN"   "KRAS"   "NRAS"   "PTK2"   "ETS1"  
## [17] "CCND1"  "XIAP"   "STAT5A" "YAP1"   "ITGA2"  "MAPK1"  "ANLN"  
## 
## $Factor3of10
##  [1] "G6PD"   "IGFBP2" "RBM15"  "PTEN"   "GATA3"  "PEA15"  "ATM"    "BRCA2" 
##  [9] "EGFR"   "FASN"   "INPP4B" "PCNA"   "ACVRL1" "TSC1"   "PDCD4"  "CDK1"  
## [17] "XRCC1"  "IRS1"   "VHL"    "AR"     "PRDX1"  "XBP1"   "NF2"    "ERCC1" 
## [25] "TFRC"   "MSH2"   "PREX1" 
## 
## $Factor4of10
##  [1] "AKT2"   "BCL2"   "MYC"    "AKT1"   "BCL2L1" "RB1"    "XIAP"   "ETS1"  
##  [9] "MAPK8"  "ARID1A" "BID"    "PTEN"   "KRAS"   "NRAS"   "PTK2"   "ATM"   
## [17] "YWHAZ"  "CCND1"  "CDKN1A" "NCOA3"  "ITGA2"  "GAB2"  
## 
## $Factor5of10
##  [1] "EIF4EBP1" "NRAS"     "MAPK9"    "EGFR"     "ACVRL1"   "PECAM1"  
##  [7] "RAB11A"   "EEF2K"    "RAD50"    "TYMS"     "XIAP"     "PARP1"   
## [13] "ANXA7"    "IGFBP2"   "ASNS"     "RBM15"    "PTEN"     "ATM"     
## [19] "BRCA2"    "TSC1"     "TTF1"     "CDK1"     "IRS1"     "GAPDH"   
## [25] "MSH6"     "PDK1"     "ERCC1"    "TFRC"    
## 
## $Factor6of10
##  [1] "AKT1S1" "SRC"    "MAPK1"  "VASP"   "ITGA2"  "YWHAE"  "TSC1"   "ANLN"  
##  [9] "PDCD4"  "GSK3A"  "RAB11B" "KEAP1"  "XRCC1"  "PDK1"   "MAP2K1" "FOXM1" 
## [17] "ERCC1"  "G6PD"   "ASNS"   "RBM15"  "PTEN"   "GATA3"  "PEA15"  "ATM"   
## [25] "EGFR"   "IRS1"   "VHL"    "XBP1"   "GAPDH"  "MSH6"   "MYH11"  "NF2"   
## [33] "TFRC"   "PREX1" 
## 
## $Factor7of10
##  [1] "MAPK14" "ERBB3"  "AKT3"   "CDH2"   "RAD51"  "BECN1"  "BIRC2"  "ITGA2" 
##  [9] "ADAR"   "BRCA2"  "PCNA"   "CTNNB1" "ANLN"   "SHC1"   "STMN1"  "ACACB" 
## [17] "CDK1"   "E2F1"   "XRCC1"  "TYMS"   "CCNB1"  "TUBA1B" "NOTCH3" "FOXM1" 
## [25] "EZH2"   "CCNE2"  "ERRFI1" "PARP1"  "RPTOR"  "CDKN2A" "PEA15"  "INPP4B"
## [33] "ACVRL1" "NF2"   
## 
## $Factor8of10
##  [1] "ERBB3"    "EIF4EBP1" "AKT2"     "CLDN7"    "ESR1"     "GATA3"   
##  [7] "EIF4G1"   "AXL"      "MAPK1"    "BIRC2"    "XRCC5"    "LCN2"    
## [13] "CDH3"     "PDCD4"    "PTK2"     "PRRT2"    "MS4A1"    "LCK"     
## [19] "CTNNA1"   "TP63"     "NRG1"     "KRT5"     "MYH9"     "YWHAB"   
## [25] "RAB25"    "BID"      "TFRC"     "ERRFI1"   "PARP1"    "CASP9"   
## [31] "NAPSA"    "SYK"      "TFF1"     "MACC1"    "CHGA"     "KCNJ13"  
## 
## $Factor9of10
##  [1] "CASP3"    "CDH1"     "ATM"      "XIAP"     "SMAD4"    "MAPK8"   
##  [7] "TUBA1B"   "YWHAZ"    "EIF4G1"   "YWHAE"    "ARID1A"   "NDRG1"   
## [13] "INPP4B"   "TP53"     "AR"       "MAPK1"    "FASN"     "CDKN1A"  
## [19] "STAT5A"   "NF2"      "NRAS"     "ADAR"     "PREX1"    "MYH9"    
## [25] "CCND1"    "CDKN1B"   "BCL2L11"  "PARP1"    "ANXA7"    "CTNNA1"  
## [31] "EEF2"     "MTOR"     "GSK3B"    "IGF1R"    "PRDX1"    "SERPINE1"
## [37] "PRKAA1"   "PXN"      "SRSF1"    "SYP"      "TFRC"     "WWTR1"   
## [43] "YWHAB"    "MACC1"   
## 
## $Factor10of10
##  [1] "CCNE1"    "PTEN"     "CAV1"     "PIK3R1"   "CDK1"     "IDH3A"   
##  [7] "ITGA2"    "RAD51"    "RPS6KB1"  "SRSF1"    "PEA15"    "TUBA1B"  
## [13] "CHGA"     "MAPK14"   "E2F1"     "NRAS"     "ADAR"     "MYH9"    
## [19] "CCND1"    "CDKN1A"   "IRS1"     "MYC"      "EGFR"     "TP63"    
## [25] "ARAF"     "JUN"      "MSH2"     "EZH2"     "MAPK9"    "PIK3R2"  
## [31] "BRCA2"    "PTGS2"    "TYMS"     "TP53"     "AKT2"     "MAP2K1"  
## [37] "NFKB1"    "ERRFI1"   "AKT3"     "BIRC2"    "CCNB1"    "CTNNA1"  
## [43] "CTNNB1"   "EEF2"     "EIF4G1"   "FOXM1"    "GSK3B"    "IGF1R"   
## [49] "IGFBP2"   "SMAD4"    "SERPINE1" "PCNA"     "PRKAA1"   "PRKCA"   
## [55] "MAPK3"    "MAPK8"    "PXN"      "TFRC"     "TGM2"     "ARID1A"  
## [61] "BECN1"    "RAB11A"   "SQSTM1"   "ANLN"     "INPP4B"   "YWHAB"   
## [67] "FASN"     "RAB11B"   "BRAF"     "PRRT2"    "MACC1"    "NF2"
saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_mofa_top_5_percent.rds")

2. Pathway Analysis

A. GO Classification

ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]

  ggo_MF[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="MF",
    keyType="SYMBOL",
    readable=TRUE)
  
  ggo_BP[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="BP",
    keyType="SYMBOL",
    readable=TRUE)

  ggo_CC[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="CC",
    keyType="SYMBOL",
    readable=TRUE)    
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16
## [1] 17
## [1] 18
## [1] 19
## [1] 20
## [1] 21
for(z in 1:length(geneNames)) {
  print(head(ggo_MF[[z]]))
  print(head(ggo_BP[[z]]))
  print(head(ggo_CC[[z]]))
}
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/23
## GO:0003824 GO:0003824           catalytic activity    15     15/23
## GO:0005198 GO:0005198 structural molecule activity     0      0/23
## GO:0005215 GO:0005215         transporter activity     0      0/23
## GO:0005488 GO:0005488                      binding    23     23/23
## GO:0009055 GO:0009055   electron transfer activity     0      0/23
##                                                                                                                                   geneID
## GO:0003774                                                                                                                          MYH9
## GO:0003824                                              HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/XIAP/MAPK1
## GO:0005198                                                                                                                              
## GO:0005215                                                                                                                              
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0009055                                                                                                                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/23
## GO:0002376 GO:0002376 immune system process    14     14/23
## GO:0008152 GO:0008152     metabolic process    21     21/23
## GO:0009987 GO:0009987      cellular process    23     23/23
## GO:0016032 GO:0016032         viral process     3      3/23
## GO:0022414 GO:0022414  reproductive process     8      8/23
##                                                                                                                                   geneID
## GO:0000003                                                                                     AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376                                                 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/XIAP/ITGA2/MAPK1
## GO:0008152           HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0016032                                                                                                             HSPA1A/AKT1/ITGA2
## GO:0022414                                                                                     AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    13     13/23
## GO:0044423 GO:0044423           virion component     0      0/23
## GO:0110165 GO:0110165 cellular anatomical entity    23     23/23
##                                                                                                                                   geneID
## GO:0032991                                                     HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/CCND1/STAT5A/YAP1/ITGA2
## GO:0044423                                                                                                                              
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/27
## GO:0003824 GO:0003824           catalytic activity    13     13/27
## GO:0005198 GO:0005198 structural molecule activity     1      1/27
## GO:0005215 GO:0005215         transporter activity     0      0/27
## GO:0005488 GO:0005488                      binding    27     27/27
## GO:0009055 GO:0009055   electron transfer activity     0      0/27
##                                                                                                                                                        geneID
## GO:0003774                                                                                                                                                   
## GO:0003824                                                                              XIAP/MAPK8/NCOA3/G6PD/ATM/BRCA2/FASN/INPP4B/VHL/PRDX1/GAPDH/MSH6/MSH2
## GO:0005198                                                                                                                                             CTNNA1
## GO:0005215                                                                                                                                                   
## GO:0005488 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/NCOA3/GAB2/STMN1/CTNNA1/G6PD/IGFBP2/RBM15/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0009055                                                                                                                                                   
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     7      7/27
## GO:0002376 GO:0002376 immune system process    19     19/27
## GO:0008152 GO:0008152     metabolic process    23     23/27
## GO:0009987 GO:0009987      cellular process    27     27/27
## GO:0016032 GO:0016032         viral process     1      1/27
## GO:0022414 GO:0022414  reproductive process     7      7/27
##                                                                                                                                                        geneID
## GO:0000003                                                                                                              RB1/CTNNA1/IGFBP2/ATM/BRCA2/MSH6/MSH2
## GO:0002376                                               RB1/XIAP/ETS1/MAPK8/ARID1A/BID/GAB2/G6PD/IGFBP2/RBM15/ATM/TSC1/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0008152                          RB1/XIAP/ETS1/MAPK8/ARID1A/BID/NCOA3/G6PD/RBM15/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0009987 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/NCOA3/GAB2/STMN1/CTNNA1/G6PD/IGFBP2/RBM15/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0016032                                                                                                                                               TFRC
## GO:0022414                                                                                                              RB1/CTNNA1/IGFBP2/ATM/BRCA2/MSH6/MSH2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    14     14/27
## GO:0044423 GO:0044423           virion component     0      0/27
## GO:0110165 GO:0110165 cellular anatomical entity    27     27/27
##                                                                                                                                                        geneID
## GO:0032991                                                                        RB1/ETS1/ARID1A/NCOA3/CTNNA1/RBM15/ATM/BRCA2/TSC1/XBP1/GAPDH/MSH6/TFRC/MSH2
## GO:0044423                                                                                                                                                   
## GO:0110165 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/NCOA3/GAB2/STMN1/CTNNA1/G6PD/IGFBP2/RBM15/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/23
## GO:0003824 GO:0003824           catalytic activity    15     15/23
## GO:0005198 GO:0005198 structural molecule activity     0      0/23
## GO:0005215 GO:0005215         transporter activity     0      0/23
## GO:0005488 GO:0005488                      binding    23     23/23
## GO:0009055 GO:0009055   electron transfer activity     0      0/23
##                                                                                                                                   geneID
## GO:0003774                                                                                                                          MYH9
## GO:0003824                                              HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/XIAP/MAPK1
## GO:0005198                                                                                                                              
## GO:0005215                                                                                                                              
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0009055                                                                                                                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/23
## GO:0002376 GO:0002376 immune system process    14     14/23
## GO:0008152 GO:0008152     metabolic process    21     21/23
## GO:0009987 GO:0009987      cellular process    23     23/23
## GO:0016032 GO:0016032         viral process     3      3/23
## GO:0022414 GO:0022414  reproductive process     8      8/23
##                                                                                                                                   geneID
## GO:0000003                                                                                     AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376                                                 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/XIAP/ITGA2/MAPK1
## GO:0008152           HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0016032                                                                                                             HSPA1A/AKT1/ITGA2
## GO:0022414                                                                                     AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    13     13/23
## GO:0044423 GO:0044423           virion component     0      0/23
## GO:0110165 GO:0110165 cellular anatomical entity    23     23/23
##                                                                                                                                   geneID
## GO:0032991                                                     HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/CCND1/STAT5A/YAP1/ITGA2
## GO:0044423                                                                                                                              
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/23
## GO:0003824 GO:0003824           catalytic activity    15     15/23
## GO:0005198 GO:0005198 structural molecule activity     0      0/23
## GO:0005215 GO:0005215         transporter activity     0      0/23
## GO:0005488 GO:0005488                      binding    23     23/23
## GO:0009055 GO:0009055   electron transfer activity     0      0/23
##                                                                                                                                   geneID
## GO:0003774                                                                                                                          MYH9
## GO:0003824                                              HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/XIAP/MAPK1
## GO:0005198                                                                                                                              
## GO:0005215                                                                                                                              
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0009055                                                                                                                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/23
## GO:0002376 GO:0002376 immune system process    14     14/23
## GO:0008152 GO:0008152     metabolic process    21     21/23
## GO:0009987 GO:0009987      cellular process    23     23/23
## GO:0016032 GO:0016032         viral process     3      3/23
## GO:0022414 GO:0022414  reproductive process     8      8/23
##                                                                                                                                   geneID
## GO:0000003                                                                                     AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376                                                 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/XIAP/ITGA2/MAPK1
## GO:0008152           HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0016032                                                                                                             HSPA1A/AKT1/ITGA2
## GO:0022414                                                                                     AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    13     13/23
## GO:0044423 GO:0044423           virion component     0      0/23
## GO:0110165 GO:0110165 cellular anatomical entity    23     23/23
##                                                                                                                                   geneID
## GO:0032991                                                     HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/CCND1/STAT5A/YAP1/ITGA2
## GO:0044423                                                                                                                              
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/20
## GO:0003824 GO:0003824           catalytic activity    11     11/20
## GO:0005198 GO:0005198 structural molecule activity     0      0/20
## GO:0005215 GO:0005215         transporter activity     0      0/20
## GO:0005488 GO:0005488                      binding    20     20/20
## GO:0009055 GO:0009055   electron transfer activity     0      0/20
##                                                                                                               geneID
## GO:0003774                                                                                                          
## GO:0003824                                                 XIAP/MAPK8/PTEN/KRAS/NRAS/PTK2/ATM/CCND1/CDKN1A/NCOA3/VHL
## GO:0005198                                                                                                          
## GO:0005215                                                                                                          
## GO:0005488 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/GAB2/ITGA2/RBM15/TSC1/VHL
## GO:0009055                                                                                                          
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     4      4/20
## GO:0002376 GO:0002376 immune system process    14     14/20
## GO:0008152 GO:0008152     metabolic process    18     18/20
## GO:0009987 GO:0009987      cellular process    20     20/20
## GO:0016032 GO:0016032         viral process     1      1/20
## GO:0022414 GO:0022414  reproductive process     4      4/20
##                                                                                                               geneID
## GO:0000003                                                                                        RB1/PTEN/ATM/ITGA2
## GO:0002376                                RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/CDKN1A/GAB2/ITGA2/RBM15/TSC1
## GO:0008152           RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/RBM15/TSC1/VHL
## GO:0009987 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/GAB2/ITGA2/RBM15/TSC1/VHL
## GO:0016032                                                                                                     ITGA2
## GO:0022414                                                                                        RB1/PTEN/ATM/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    10     10/20
## GO:0044423 GO:0044423           virion component     0      0/20
## GO:0110165 GO:0110165 cellular anatomical entity    20     20/20
##                                                                                                               geneID
## GO:0032991                                                   RB1/ETS1/ARID1A/ATM/CCND1/CDKN1A/NCOA3/ITGA2/RBM15/TSC1
## GO:0044423                                                                                                          
## GO:0110165 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/GAB2/ITGA2/RBM15/TSC1/VHL
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/36
## GO:0003824 GO:0003824           catalytic activity    13     13/36
## GO:0005198 GO:0005198 structural molecule activity     2      2/36
## GO:0005215 GO:0005215         transporter activity     1      1/36
## GO:0005488 GO:0005488                      binding    34     34/36
## GO:0009055 GO:0009055   electron transfer activity     0      0/36
##                                                                                                                                                                                                        geneID
## GO:0003774                                                                                                                                                                                               MYH9
## GO:0003824                                                                                                                            RAD51/BIRC2/XRCC5/ADAR/BRCA2/PTK2/CDK1/LCK/GAPDH/EZH2/RAB25/PARP1/NAPSA
## GO:0005198                                                                                                                                                                                        CTNNA1/KRT5
## GO:0005215                                                                                                                                                                                             KCNJ13
## GO:0005488 ERBB3/EIF4EBP1/RAD51/GATA3/EIF4G1/BIRC2/XRCC5/ADAR/BRCA2/CDH3/PDCD4/PTK2/PRRT2/CDK1/MS4A1/LCK/CTNNA1/AR/TP63/GAPDH/CCNB1/KRT5/MYH9/FOXM1/YWHAB/EZH2/RAB25/TFRC/CCNE2/ERRFI1/PARP1/NAPSA/TFF1/MACC1
## GO:0009055                                                                                                                                                                                                   
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    11     11/36
## GO:0002376 GO:0002376 immune system process    13     13/36
## GO:0008152 GO:0008152     metabolic process    29     29/36
## GO:0009987 GO:0009987      cellular process    35     35/36
## GO:0016032 GO:0016032         viral process     3      3/36
## GO:0022414 GO:0022414  reproductive process    11     11/36
##                                                                                                                                                                                                              geneID
## GO:0000003                                                                                                                                            RAD51/GATA3/BRCA2/CDK1/CTNNA1/AR/TP63/MYH9/CCNE2/ERRFI1/PARP1
## GO:0002376                                                                                                                                    GATA3/BIRC2/XRCC5/ADAR/PTK2/MS4A1/LCK/GAPDH/MYH9/EZH2/TFRC/PARP1/CHGA
## GO:0008152                                     ERBB3/EIF4EBP1/RAD51/GATA3/EIF4G1/BIRC2/XRCC5/ADAR/BRCA2/CDH3/PDCD4/PTK2/CDK1/LCK/AR/TP63/GAPDH/CCNB1/MYH9/FOXM1/YWHAB/EZH2/TFRC/CCNE2/ERRFI1/PARP1/NAPSA/TFF1/MACC1
## GO:0009987 ERBB3/EIF4EBP1/RAD51/GATA3/EIF4G1/BIRC2/XRCC5/ADAR/BRCA2/CDH3/PDCD4/PTK2/PRRT2/CDK1/MS4A1/LCK/CTNNA1/AR/TP63/GAPDH/CCNB1/KRT5/MYH9/FOXM1/YWHAB/EZH2/RAB25/TFRC/CCNE2/ERRFI1/PARP1/TFF1/MACC1/CHGA/KCNJ13
## GO:0016032                                                                                                                                                                                           ADAR/CDK1/TFRC
## GO:0022414                                                                                                                                            RAD51/GATA3/BRCA2/CDK1/CTNNA1/AR/TP63/MYH9/CCNE2/ERRFI1/PARP1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    22     22/36
## GO:0044423 GO:0044423           virion component     0      0/36
## GO:0110165 GO:0110165 cellular anatomical entity    36     36/36
##                                                                                                                                                                                                                    geneID
## GO:0032991                                                                                   ERBB3/RAD51/GATA3/EIF4G1/BIRC2/XRCC5/ADAR/BRCA2/CDH3/CDK1/CTNNA1/AR/TP63/GAPDH/CCNB1/MYH9/FOXM1/EZH2/TFRC/CCNE2/PARP1/KCNJ13
## GO:0044423                                                                                                                                                                                                               
## GO:0110165 ERBB3/EIF4EBP1/RAD51/GATA3/EIF4G1/BIRC2/XRCC5/ADAR/BRCA2/CDH3/PDCD4/PTK2/PRRT2/CDK1/MS4A1/LCK/CTNNA1/AR/TP63/GAPDH/CCNB1/KRT5/MYH9/FOXM1/YWHAB/EZH2/RAB25/TFRC/CCNE2/ERRFI1/PARP1/NAPSA/TFF1/MACC1/CHGA/KCNJ13
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/30
## GO:0003824 GO:0003824           catalytic activity    14     14/30
## GO:0005198 GO:0005198 structural molecule activity     2      2/30
## GO:0005215 GO:0005215         transporter activity     0      0/30
## GO:0005488 GO:0005488                      binding    30     30/30
## GO:0009055 GO:0009055   electron transfer activity     0      0/30
##                                                                                                                                                                             geneID
## GO:0003774                                                                                                                                                                   MYH11
## GO:0003824                                                                                             FASN/PRKCA/CDK1/TYMS/G6PD/ATM/BRCA2/INPP4B/ACVRL1/VHL/PRDX1/GAPDH/MSH6/MSH2
## GO:0005198                                                                                                                                                            CTNNA1/MYH11
## GO:0005215                                                                                                                                                                        
## GO:0005488 FASN/PRKCA/ANLN/STMN1/CDK1/CTNNA1/TYMS/CCNB1/FOXM1/YWHAB/G6PD/IGFBP2/RBM15/GATA3/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/IRS1/VHL/PRDX1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2/PREX1
## GO:0009055                                                                                                                                                                        
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/30
## GO:0002376 GO:0002376 immune system process    14     14/30
## GO:0008152 GO:0008152     metabolic process    25     25/30
## GO:0009987 GO:0009987      cellular process    30     30/30
## GO:0016032 GO:0016032         viral process     2      2/30
## GO:0022414 GO:0022414  reproductive process     8      8/30
##                                                                                                                                                                             geneID
## GO:0000003                                                                                                                            CDK1/CTNNA1/IGFBP2/GATA3/ATM/BRCA2/MSH6/MSH2
## GO:0002376                                                                                            PRKCA/G6PD/IGFBP2/RBM15/GATA3/ATM/TSC1/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0008152                                FASN/PRKCA/CDK1/TYMS/CCNB1/FOXM1/YWHAB/G6PD/RBM15/GATA3/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/IRS1/VHL/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0009987 FASN/PRKCA/ANLN/STMN1/CDK1/CTNNA1/TYMS/CCNB1/FOXM1/YWHAB/G6PD/IGFBP2/RBM15/GATA3/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/IRS1/VHL/PRDX1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2/PREX1
## GO:0016032                                                                                                                                                               CDK1/TFRC
## GO:0022414                                                                                                                            CDK1/CTNNA1/IGFBP2/GATA3/ATM/BRCA2/MSH6/MSH2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    18     18/30
## GO:0044423 GO:0044423           virion component     0      0/30
## GO:0110165 GO:0110165 cellular anatomical entity    30     30/30
##                                                                                                                                                                             geneID
## GO:0032991                                                                    PRKCA/CDK1/CTNNA1/CCNB1/FOXM1/RBM15/GATA3/ATM/BRCA2/ACVRL1/TSC1/IRS1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2
## GO:0044423                                                                                                                                                                        
## GO:0110165 FASN/PRKCA/ANLN/STMN1/CDK1/CTNNA1/TYMS/CCNB1/FOXM1/YWHAB/G6PD/IGFBP2/RBM15/GATA3/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/IRS1/VHL/PRDX1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2/PREX1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/23
## GO:0003824 GO:0003824           catalytic activity    15     15/23
## GO:0005198 GO:0005198 structural molecule activity     0      0/23
## GO:0005215 GO:0005215         transporter activity     0      0/23
## GO:0005488 GO:0005488                      binding    23     23/23
## GO:0009055 GO:0009055   electron transfer activity     0      0/23
##                                                                                                                                   geneID
## GO:0003774                                                                                                                          MYH9
## GO:0003824                                              HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/XIAP/MAPK1
## GO:0005198                                                                                                                              
## GO:0005215                                                                                                                              
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0009055                                                                                                                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/23
## GO:0002376 GO:0002376 immune system process    14     14/23
## GO:0008152 GO:0008152     metabolic process    21     21/23
## GO:0009987 GO:0009987      cellular process    23     23/23
## GO:0016032 GO:0016032         viral process     3      3/23
## GO:0022414 GO:0022414  reproductive process     8      8/23
##                                                                                                                                   geneID
## GO:0000003                                                                                     AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376                                                 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/XIAP/ITGA2/MAPK1
## GO:0008152           HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0016032                                                                                                             HSPA1A/AKT1/ITGA2
## GO:0022414                                                                                     AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    13     13/23
## GO:0044423 GO:0044423           virion component     0      0/23
## GO:0110165 GO:0110165 cellular anatomical entity    23     23/23
##                                                                                                                                   geneID
## GO:0032991                                                     HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/CCND1/STAT5A/YAP1/ITGA2
## GO:0044423                                                                                                                              
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/17
## GO:0003824 GO:0003824           catalytic activity    10     10/17
## GO:0005198 GO:0005198 structural molecule activity     0      0/17
## GO:0005215 GO:0005215         transporter activity     0      0/17
## GO:0005488 GO:0005488                      binding    17     17/17
## GO:0009055 GO:0009055   electron transfer activity     0      0/17
##                                                                                                geneID
## GO:0003774                                                                                           
## GO:0003824                                      XIAP/MAPK8/PTEN/KRAS/NRAS/PTK2/ATM/CCND1/CDKN1A/NCOA3
## GO:0005198                                                                                           
## GO:0005215                                                                                           
## GO:0005488 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/GAB2
## GO:0009055                                                                                           
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     4      4/17
## GO:0002376 GO:0002376 immune system process    12     12/17
## GO:0008152 GO:0008152     metabolic process    15     15/17
## GO:0009987 GO:0009987      cellular process    17     17/17
## GO:0016032 GO:0016032         viral process     1      1/17
## GO:0022414 GO:0022414  reproductive process     4      4/17
##                                                                                                geneID
## GO:0000003                                                                         RB1/PTEN/ATM/ITGA2
## GO:0002376                            RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/CDKN1A/ITGA2/GAB2
## GO:0008152           RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2
## GO:0009987 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/GAB2
## GO:0016032                                                                                      ITGA2
## GO:0022414                                                                         RB1/PTEN/ATM/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     8      8/17
## GO:0044423 GO:0044423           virion component     0      0/17
## GO:0110165 GO:0110165 cellular anatomical entity    17     17/17
##                                                                                                geneID
## GO:0032991                                               RB1/ETS1/ARID1A/ATM/CCND1/CDKN1A/NCOA3/ITGA2
## GO:0044423                                                                                           
## GO:0110165 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/GAB2
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/62
## GO:0003824 GO:0003824           catalytic activity    29     29/62
## GO:0005198 GO:0005198 structural molecule activity     2      2/62
## GO:0005215 GO:0005215         transporter activity     1      1/62
## GO:0005488 GO:0005488                      binding    62     62/62
## GO:0009055 GO:0009055   electron transfer activity     0      0/62
##                                                                                                                                                                                                                                                                                                                                                                       geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                                              MYH9
## GO:0003824                                                                                                                                                                                                     EGFR/MET/AKT1/IGF1R/CASP3/ATM/XIAP/MAPK8/TUBA1B/CASP8/RAD51/ACVRL1/NCOA3/PARP1/NRAS/MTOR/PRDX1/PRKAA1/ERBB2/ADAR/AKT2/EEF2/GAPDH/FASN/G6PD/PTEN/CDK1/VHL/MSH2
## GO:0005198                                                                                                                                                                                                                                                                                                                                                     TUBA1B/CTNNA1
## GO:0005215                                                                                                                                                                                                                                                                                                                                                             IGF1R
## GO:0005488 EGFR/MET/AKT1/BCL2L1/IGF1R/CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/TUBA1B/RB1/NF2/E2F1/MYH9/MYC/YWHAZ/CASP8/RAD51/NDRG1/ACVRL1/NCOA3/PARP1/EIF4EBP1/NRAS/CDKN1B/CTNNA1/MTOR/PRDX1/SERPINE1/PRKAA1/PXN/SRSF1/TFRC/YWHAB/ERBB2/ADAR/JUN/NOTCH3/BCL2L11/TP53/AKT2/XBP1/STAT3/EEF2/EIF4G1/GAPDH/VASP/ARID1A/AKT1S1/RICTOR/PTCH1/FASN/G6PD/PTEN/PEA15/CDK1/IRS1/VHL/MSH2/PREX1
## GO:0009055                                                                                                                                                                                                                                                                                                                                                                  
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    21     21/62
## GO:0002376 GO:0002376 immune system process    28     28/62
## GO:0008152 GO:0008152     metabolic process    53     53/62
## GO:0009987 GO:0009987      cellular process    62     62/62
## GO:0016032 GO:0016032         viral process     7      7/62
## GO:0022414 GO:0022414  reproductive process    20     20/62
##                                                                                                                                                                                                                                                                                                                                                                       geneID
## GO:0000003                                                                                                                                                                                                                                           EGFR/AKT1/BCL2L1/IGF1R/CASP3/ATM/SMAD4/RB1/MYH9/CASP8/RAD51/PARP1/CDKN1B/CTNNA1/MTOR/BCL2L11/STAT3/PTCH1/PTEN/CDK1/MSH2
## GO:0002376                                                                                                                                                                                                     AKT1/IGF1R/CASP3/ATM/XIAP/MAPK8/RB1/MYH9/MYC/YWHAZ/CASP8/NDRG1/PARP1/MTOR/PRDX1/SERPINE1/TFRC/ERBB2/ADAR/BCL2L11/TP53/XBP1/STAT3/GAPDH/ARID1A/G6PD/MSH2/PREX1
## GO:0008152                                                        EGFR/MET/AKT1/IGF1R/CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/RB1/NF2/E2F1/MYH9/MYC/YWHAZ/CASP8/RAD51/ACVRL1/NCOA3/PARP1/EIF4EBP1/CDKN1B/MTOR/PRDX1/SERPINE1/PRKAA1/SRSF1/TFRC/YWHAB/ERBB2/ADAR/JUN/NOTCH3/TP53/AKT2/XBP1/STAT3/EEF2/EIF4G1/GAPDH/ARID1A/AKT1S1/RICTOR/PTCH1/FASN/G6PD/PTEN/CDK1/IRS1/VHL/MSH2/PREX1
## GO:0009987 EGFR/MET/AKT1/BCL2L1/IGF1R/CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/TUBA1B/RB1/NF2/E2F1/MYH9/MYC/YWHAZ/CASP8/RAD51/NDRG1/ACVRL1/NCOA3/PARP1/EIF4EBP1/NRAS/CDKN1B/CTNNA1/MTOR/PRDX1/SERPINE1/PRKAA1/PXN/SRSF1/TFRC/YWHAB/ERBB2/ADAR/JUN/NOTCH3/BCL2L11/TP53/AKT2/XBP1/STAT3/EEF2/EIF4G1/GAPDH/VASP/ARID1A/AKT1S1/RICTOR/PTCH1/FASN/G6PD/PTEN/PEA15/CDK1/IRS1/VHL/MSH2/PREX1
## GO:0016032                                                                                                                                                                                                                                                                                                                                 EGFR/AKT1/TFRC/ADAR/JUN/TP53/CDK1
## GO:0022414                                                                                                                                                                                                                                                 EGFR/AKT1/BCL2L1/IGF1R/CASP3/ATM/SMAD4/RB1/MYH9/CASP8/RAD51/PARP1/CDKN1B/CTNNA1/MTOR/BCL2L11/PTCH1/PTEN/CDK1/MSH2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    44     44/62
## GO:0044423 GO:0044423           virion component     0      0/62
## GO:0110165 GO:0110165 cellular anatomical entity    62     62/62
##                                                                                                                                                                                                                                                                                                                                                                       geneID
## GO:0032991                                                                                                      EGFR/MET/AKT1/BCL2L1/IGF1R/CASP3/CDH1/ATM/SMAD4/RB1/E2F1/MYH9/MYC/CASP8/RAD51/ACVRL1/NCOA3/PARP1/CDKN1B/CTNNA1/MTOR/SERPINE1/PRKAA1/PXN/SRSF1/TFRC/ERBB2/ADAR/JUN/NOTCH3/BCL2L11/TP53/XBP1/STAT3/EEF2/EIF4G1/GAPDH/ARID1A/AKT1S1/RICTOR/PEA15/CDK1/IRS1/MSH2
## GO:0044423                                                                                                                                                                                                                                                                                                                                                                  
## GO:0110165 EGFR/MET/AKT1/BCL2L1/IGF1R/CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/TUBA1B/RB1/NF2/E2F1/MYH9/MYC/YWHAZ/CASP8/RAD51/NDRG1/ACVRL1/NCOA3/PARP1/EIF4EBP1/NRAS/CDKN1B/CTNNA1/MTOR/PRDX1/SERPINE1/PRKAA1/PXN/SRSF1/TFRC/YWHAB/ERBB2/ADAR/JUN/NOTCH3/BCL2L11/TP53/AKT2/XBP1/STAT3/EEF2/EIF4G1/GAPDH/VASP/ARID1A/AKT1S1/RICTOR/PTCH1/FASN/G6PD/PTEN/PEA15/CDK1/IRS1/VHL/MSH2/PREX1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/36
## GO:0003824 GO:0003824           catalytic activity    14     14/36
## GO:0005198 GO:0005198 structural molecule activity     1      1/36
## GO:0005215 GO:0005215         transporter activity     1      1/36
## GO:0005488 GO:0005488                      binding    34     34/36
## GO:0009055 GO:0009055   electron transfer activity     0      0/36
##                                                                                                                                                                                                   geneID
## GO:0003774                                                                                                                                                                                          MYH9
## GO:0003824                                                                                                              MAPK14/AKT2/RAD51/MAPK1/BIRC2/XRCC5/BRCA2/PTK2/LCK/GAPDH/RAB25/ERCC1/PARP1/NAPSA
## GO:0005198                                                                                                                                                                                          KRT5
## GO:0005215                                                                                                                                                                                        KCNJ13
## GO:0005488 MAPK14/ERBB3/AKT2/RAD51/GATA3/EIF4G1/MAPK1/BIRC2/XRCC5/BRCA2/LCN2/CDH3/PDCD4/PTK2/PRRT2/MS4A1/LCK/AR/TP63/GAPDH/NRG1/KRT5/MYH9/FOXM1/YWHAB/RAB25/ERCC1/BID/TFRC/ERRFI1/PARP1/NAPSA/TFF1/MACC1
## GO:0009055                                                                                                                                                                                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     9      9/36
## GO:0002376 GO:0002376 immune system process    16     16/36
## GO:0008152 GO:0008152     metabolic process    30     30/36
## GO:0009987 GO:0009987      cellular process    35     35/36
## GO:0016032 GO:0016032         viral process     1      1/36
## GO:0022414 GO:0022414  reproductive process     9      9/36
##                                                                                                                                                                                                         geneID
## GO:0000003                                                                                                                                                   RAD51/GATA3/BRCA2/AR/TP63/MYH9/ERCC1/ERRFI1/PARP1
## GO:0002376                                                                                                             MAPK14/GATA3/MAPK1/BIRC2/XRCC5/LCN2/PTK2/MS4A1/LCK/GAPDH/MYH9/ERCC1/BID/TFRC/PARP1/CHGA
## GO:0008152                              MAPK14/ERBB3/AKT2/RAD51/GATA3/EIF4G1/MAPK1/BIRC2/XRCC5/BRCA2/LCN2/CDH3/PDCD4/PTK2/LCK/AR/TP63/GAPDH/NRG1/MYH9/FOXM1/YWHAB/ERCC1/BID/TFRC/ERRFI1/PARP1/NAPSA/TFF1/MACC1
## GO:0009987 MAPK14/ERBB3/AKT2/RAD51/GATA3/EIF4G1/MAPK1/BIRC2/XRCC5/BRCA2/LCN2/CDH3/PDCD4/PTK2/PRRT2/MS4A1/LCK/AR/TP63/GAPDH/NRG1/KRT5/MYH9/FOXM1/YWHAB/RAB25/ERCC1/BID/TFRC/ERRFI1/PARP1/TFF1/MACC1/CHGA/KCNJ13
## GO:0016032                                                                                                                                                                                                TFRC
## GO:0022414                                                                                                                                                   RAD51/GATA3/BRCA2/AR/TP63/MYH9/ERCC1/ERRFI1/PARP1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    17     17/36
## GO:0044423 GO:0044423           virion component     0      0/36
## GO:0110165 GO:0110165 cellular anatomical entity    36     36/36
##                                                                                                                                                                                                               geneID
## GO:0032991                                                                                                          ERBB3/RAD51/GATA3/EIF4G1/BIRC2/XRCC5/BRCA2/CDH3/AR/TP63/GAPDH/MYH9/FOXM1/ERCC1/TFRC/PARP1/KCNJ13
## GO:0044423                                                                                                                                                                                                          
## GO:0110165 MAPK14/ERBB3/AKT2/RAD51/GATA3/EIF4G1/MAPK1/BIRC2/XRCC5/BRCA2/LCN2/CDH3/PDCD4/PTK2/PRRT2/MS4A1/LCK/AR/TP63/GAPDH/NRG1/KRT5/MYH9/FOXM1/YWHAB/RAB25/ERCC1/BID/TFRC/ERRFI1/PARP1/NAPSA/TFF1/MACC1/CHGA/KCNJ13
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/27
## GO:0003824 GO:0003824           catalytic activity    14     14/27
## GO:0005198 GO:0005198 structural molecule activity     2      2/27
## GO:0005215 GO:0005215         transporter activity     0      0/27
## GO:0005488 GO:0005488                      binding    27     27/27
## GO:0009055 GO:0009055   electron transfer activity     0      0/27
##                                                                                                                                                           geneID
## GO:0003774                                                                                                                                                 MYH11
## GO:0003824                                                                             FASN/PRKCA/CDK1/TYMS/MSH6/G6PD/ASNS/ATM/BRCA2/INPP4B/VHL/PRDX1/GAPDH/MSH2
## GO:0005198                                                                                                                                          CTNNA1/MYH11
## GO:0005215                                                                                                                                                      
## GO:0005488 FASN/PRKCA/STMN1/CDK1/CTNNA1/TYMS/MSH6/CCNB1/PREX1/G6PD/IGFBP2/ASNS/RBM15/GATA3/PEA15/ATM/BRCA2/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MYH11/TFRC/MSH2
## GO:0009055                                                                                                                                                      
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/27
## GO:0002376 GO:0002376 immune system process    14     14/27
## GO:0008152 GO:0008152     metabolic process    22     22/27
## GO:0009987 GO:0009987      cellular process    27     27/27
## GO:0016032 GO:0016032         viral process     2      2/27
## GO:0022414 GO:0022414  reproductive process     8      8/27
##                                                                                                                                                           geneID
## GO:0000003                                                                                                          CDK1/CTNNA1/MSH6/IGFBP2/GATA3/ATM/BRCA2/MSH2
## GO:0002376                                                                          PRKCA/MSH6/PREX1/G6PD/IGFBP2/RBM15/GATA3/ATM/TSC1/PRDX1/XBP1/GAPDH/TFRC/MSH2
## GO:0008152                                 FASN/PRKCA/CDK1/TYMS/MSH6/CCNB1/PREX1/G6PD/ASNS/RBM15/GATA3/ATM/BRCA2/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/TFRC/MSH2
## GO:0009987 FASN/PRKCA/STMN1/CDK1/CTNNA1/TYMS/MSH6/CCNB1/PREX1/G6PD/IGFBP2/ASNS/RBM15/GATA3/PEA15/ATM/BRCA2/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MYH11/TFRC/MSH2
## GO:0016032                                                                                                                                             CDK1/TFRC
## GO:0022414                                                                                                          CDK1/CTNNA1/MSH6/IGFBP2/GATA3/ATM/BRCA2/MSH2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    16     16/27
## GO:0044423 GO:0044423           virion component     0      0/27
## GO:0110165 GO:0110165 cellular anatomical entity    27     27/27
##                                                                                                                                                           geneID
## GO:0032991                                                              PRKCA/CDK1/CTNNA1/MSH6/CCNB1/RBM15/GATA3/PEA15/ATM/BRCA2/TSC1/XBP1/GAPDH/MYH11/TFRC/MSH2
## GO:0044423                                                                                                                                                      
## GO:0110165 FASN/PRKCA/STMN1/CDK1/CTNNA1/TYMS/MSH6/CCNB1/PREX1/G6PD/IGFBP2/ASNS/RBM15/GATA3/PEA15/ATM/BRCA2/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MYH11/TFRC/MSH2
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/23
## GO:0003824 GO:0003824           catalytic activity    15     15/23
## GO:0005198 GO:0005198 structural molecule activity     0      0/23
## GO:0005215 GO:0005215         transporter activity     0      0/23
## GO:0005488 GO:0005488                      binding    23     23/23
## GO:0009055 GO:0009055   electron transfer activity     0      0/23
##                                                                                                                                   geneID
## GO:0003774                                                                                                                          MYH9
## GO:0003824                                              HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/XIAP/MAPK1
## GO:0005198                                                                                                                              
## GO:0005215                                                                                                                              
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0009055                                                                                                                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/23
## GO:0002376 GO:0002376 immune system process    14     14/23
## GO:0008152 GO:0008152     metabolic process    21     21/23
## GO:0009987 GO:0009987      cellular process    23     23/23
## GO:0016032 GO:0016032         viral process     3      3/23
## GO:0022414 GO:0022414  reproductive process     8      8/23
##                                                                                                                                   geneID
## GO:0000003                                                                                     AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376                                                 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/XIAP/ITGA2/MAPK1
## GO:0008152           HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0016032                                                                                                             HSPA1A/AKT1/ITGA2
## GO:0022414                                                                                     AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    13     13/23
## GO:0044423 GO:0044423           virion component     0      0/23
## GO:0110165 GO:0110165 cellular anatomical entity    23     23/23
##                                                                                                                                   geneID
## GO:0032991                                                     HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/CCND1/STAT5A/YAP1/ITGA2
## GO:0044423                                                                                                                              
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/27
## GO:0003824 GO:0003824           catalytic activity    15     15/27
## GO:0005198 GO:0005198 structural molecule activity     0      0/27
## GO:0005215 GO:0005215         transporter activity     0      0/27
## GO:0005488 GO:0005488                      binding    27     27/27
## GO:0009055 GO:0009055   electron transfer activity     0      0/27
##                                                                                                                                                      geneID
## GO:0003774                                                                                                                                                 
## GO:0003824                                                                 G6PD/PTEN/ATM/BRCA2/EGFR/FASN/INPP4B/PCNA/ACVRL1/CDK1/XRCC1/VHL/PRDX1/ERCC1/MSH2
## GO:0005198                                                                                                                                                 
## GO:0005215                                                                                                                                                 
## GO:0005488 G6PD/IGFBP2/RBM15/PTEN/GATA3/PEA15/ATM/BRCA2/EGFR/FASN/INPP4B/PCNA/ACVRL1/TSC1/PDCD4/CDK1/XRCC1/IRS1/VHL/AR/PRDX1/XBP1/NF2/ERCC1/TFRC/MSH2/PREX1
## GO:0009055                                                                                                                                                 
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    11     11/27
## GO:0002376 GO:0002376 immune system process    12     12/27
## GO:0008152 GO:0008152     metabolic process    25     25/27
## GO:0009987 GO:0009987      cellular process    27     27/27
## GO:0016032 GO:0016032         viral process     3      3/27
## GO:0022414 GO:0022414  reproductive process    11     11/27
##                                                                                                                                                      geneID
## GO:0000003                                                                                         IGFBP2/PTEN/GATA3/ATM/BRCA2/EGFR/PCNA/CDK1/AR/ERCC1/MSH2
## GO:0002376                                                                                G6PD/IGFBP2/RBM15/GATA3/ATM/TSC1/PRDX1/XBP1/ERCC1/TFRC/MSH2/PREX1
## GO:0008152              G6PD/RBM15/PTEN/GATA3/ATM/BRCA2/EGFR/FASN/INPP4B/PCNA/ACVRL1/TSC1/PDCD4/CDK1/XRCC1/IRS1/VHL/AR/PRDX1/XBP1/NF2/ERCC1/TFRC/MSH2/PREX1
## GO:0009987 G6PD/IGFBP2/RBM15/PTEN/GATA3/PEA15/ATM/BRCA2/EGFR/FASN/INPP4B/PCNA/ACVRL1/TSC1/PDCD4/CDK1/XRCC1/IRS1/VHL/AR/PRDX1/XBP1/NF2/ERCC1/TFRC/MSH2/PREX1
## GO:0016032                                                                                                                                   EGFR/CDK1/TFRC
## GO:0022414                                                                                         IGFBP2/PTEN/GATA3/ATM/BRCA2/EGFR/PCNA/CDK1/AR/ERCC1/MSH2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    17     17/27
## GO:0044423 GO:0044423           virion component     0      0/27
## GO:0110165 GO:0110165 cellular anatomical entity    27     27/27
##                                                                                                                                                      geneID
## GO:0032991                                                        RBM15/GATA3/PEA15/ATM/BRCA2/EGFR/PCNA/ACVRL1/TSC1/CDK1/XRCC1/IRS1/AR/XBP1/ERCC1/TFRC/MSH2
## GO:0044423                                                                                                                                                 
## GO:0110165 G6PD/IGFBP2/RBM15/PTEN/GATA3/PEA15/ATM/BRCA2/EGFR/FASN/INPP4B/PCNA/ACVRL1/TSC1/PDCD4/CDK1/XRCC1/IRS1/VHL/AR/PRDX1/XBP1/NF2/ERCC1/TFRC/MSH2/PREX1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/22
## GO:0003824 GO:0003824           catalytic activity    12     12/22
## GO:0005198 GO:0005198 structural molecule activity     0      0/22
## GO:0005215 GO:0005215         transporter activity     1      1/22
## GO:0005488 GO:0005488                      binding    22     22/22
## GO:0009055 GO:0009055   electron transfer activity     0      0/22
##                                                                                                                          geneID
## GO:0003774                                                                                                                     
## GO:0003824                                                      AKT2/AKT1/XIAP/MAPK8/PTEN/KRAS/NRAS/PTK2/ATM/CCND1/CDKN1A/NCOA3
## GO:0005198                                                                                                                     
## GO:0005215                                                                                                                 BCL2
## GO:0005488 AKT2/BCL2/MYC/AKT1/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/GAB2
## GO:0009055                                                                                                                     
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     7      7/22
## GO:0002376 GO:0002376 immune system process    15     15/22
## GO:0008152 GO:0008152     metabolic process    19     19/22
## GO:0009987 GO:0009987      cellular process    22     22/22
## GO:0016032 GO:0016032         viral process     3      3/22
## GO:0022414 GO:0022414  reproductive process     7      7/22
##                                                                                                                          geneID
## GO:0000003                                                                                  BCL2/AKT1/BCL2L1/RB1/PTEN/ATM/ITGA2
## GO:0002376                                        BCL2/MYC/AKT1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/CDKN1A/ITGA2/GAB2
## GO:0008152                  AKT2/BCL2/MYC/AKT1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2
## GO:0009987 AKT2/BCL2/MYC/AKT1/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/GAB2
## GO:0016032                                                                                                      BCL2/AKT1/ITGA2
## GO:0022414                                                                                  BCL2/AKT1/BCL2L1/RB1/PTEN/ATM/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    12     12/22
## GO:0044423 GO:0044423           virion component     0      0/22
## GO:0110165 GO:0110165 cellular anatomical entity    22     22/22
##                                                                                                                          geneID
## GO:0032991                                                    BCL2/MYC/AKT1/BCL2L1/RB1/ETS1/ARID1A/ATM/CCND1/CDKN1A/NCOA3/ITGA2
## GO:0044423                                                                                                                     
## GO:0110165 AKT2/BCL2/MYC/AKT1/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/GAB2
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/28
## GO:0003824 GO:0003824           catalytic activity    19     19/28
## GO:0005198 GO:0005198 structural molecule activity     0      0/28
## GO:0005215 GO:0005215         transporter activity     0      0/28
## GO:0005488 GO:0005488                      binding    28     28/28
## GO:0009055 GO:0009055   electron transfer activity     0      0/28
##                                                                                                                                                                     geneID
## GO:0003774                                                                                                                                                                
## GO:0003824                                                        NRAS/MAPK9/EGFR/ACVRL1/RAB11A/EEF2K/RAD50/TYMS/XIAP/PARP1/ASNS/PTEN/ATM/BRCA2/CDK1/GAPDH/MSH6/PDK1/ERCC1
## GO:0005198                                                                                                                                                                
## GO:0005215                                                                                                                                                                
## GO:0005488 EIF4EBP1/NRAS/MAPK9/EGFR/ACVRL1/PECAM1/RAB11A/EEF2K/RAD50/TYMS/XIAP/PARP1/ANXA7/IGFBP2/ASNS/RBM15/PTEN/ATM/BRCA2/TSC1/TTF1/CDK1/IRS1/GAPDH/MSH6/PDK1/ERCC1/TFRC
## GO:0009055                                                                                                                                                                
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    10     10/28
## GO:0002376 GO:0002376 immune system process    12     12/28
## GO:0008152 GO:0008152     metabolic process    25     25/28
## GO:0009987 GO:0009987      cellular process    28     28/28
## GO:0016032 GO:0016032         viral process     3      3/28
## GO:0022414 GO:0022414  reproductive process    10     10/28
##                                                                                                                                                                     geneID
## GO:0000003                                                                                                          EGFR/RAD50/PARP1/IGFBP2/PTEN/ATM/BRCA2/CDK1/MSH6/ERCC1
## GO:0002376                                                                                             MAPK9/PECAM1/XIAP/PARP1/IGFBP2/RBM15/ATM/TSC1/GAPDH/MSH6/ERCC1/TFRC
## GO:0008152                    EIF4EBP1/MAPK9/EGFR/ACVRL1/PECAM1/EEF2K/RAD50/TYMS/XIAP/PARP1/ANXA7/ASNS/RBM15/PTEN/ATM/BRCA2/TSC1/TTF1/CDK1/IRS1/GAPDH/MSH6/PDK1/ERCC1/TFRC
## GO:0009987 EIF4EBP1/NRAS/MAPK9/EGFR/ACVRL1/PECAM1/RAB11A/EEF2K/RAD50/TYMS/XIAP/PARP1/ANXA7/IGFBP2/ASNS/RBM15/PTEN/ATM/BRCA2/TSC1/TTF1/CDK1/IRS1/GAPDH/MSH6/PDK1/ERCC1/TFRC
## GO:0016032                                                                                                                                                  EGFR/CDK1/TFRC
## GO:0022414                                                                                                          EGFR/RAD50/PARP1/IGFBP2/PTEN/ATM/BRCA2/CDK1/MSH6/ERCC1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    17     17/28
## GO:0044423 GO:0044423           virion component     0      0/28
## GO:0110165 GO:0110165 cellular anatomical entity    28     28/28
##                                                                                                                                                                     geneID
## GO:0032991                                                                 EGFR/ACVRL1/PECAM1/RAB11A/RAD50/PARP1/RBM15/ATM/BRCA2/TSC1/CDK1/IRS1/GAPDH/MSH6/PDK1/ERCC1/TFRC
## GO:0044423                                                                                                                                                                
## GO:0110165 EIF4EBP1/NRAS/MAPK9/EGFR/ACVRL1/PECAM1/RAB11A/EEF2K/RAD50/TYMS/XIAP/PARP1/ANXA7/IGFBP2/ASNS/RBM15/PTEN/ATM/BRCA2/TSC1/TTF1/CDK1/IRS1/GAPDH/MSH6/PDK1/ERCC1/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/34
## GO:0003824 GO:0003824           catalytic activity    16     16/34
## GO:0005198 GO:0005198 structural molecule activity     1      1/34
## GO:0005215 GO:0005215         transporter activity     0      0/34
## GO:0005488 GO:0005488                      binding    34     34/34
## GO:0009055 GO:0009055   electron transfer activity     0      0/34
##                                                                                                                                                                                                geneID
## GO:0003774                                                                                                                                                                                      MYH11
## GO:0003824                                                                                                      SRC/MAPK1/GSK3A/RAB11B/XRCC1/PDK1/MAP2K1/ERCC1/G6PD/ASNS/PTEN/ATM/EGFR/VHL/GAPDH/MSH6
## GO:0005198                                                                                                                                                                                      MYH11
## GO:0005215                                                                                                                                                                                           
## GO:0005488 AKT1S1/SRC/MAPK1/VASP/ITGA2/YWHAE/TSC1/ANLN/PDCD4/GSK3A/RAB11B/KEAP1/XRCC1/PDK1/MAP2K1/FOXM1/ERCC1/G6PD/ASNS/RBM15/PTEN/GATA3/PEA15/ATM/EGFR/IRS1/VHL/XBP1/GAPDH/MSH6/MYH11/NF2/TFRC/PREX1
## GO:0009055                                                                                                                                                                                           
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     9      9/34
## GO:0002376 GO:0002376 immune system process    16     16/34
## GO:0008152 GO:0008152     metabolic process    30     30/34
## GO:0009987 GO:0009987      cellular process    34     34/34
## GO:0016032 GO:0016032         viral process     4      4/34
## GO:0022414 GO:0022414  reproductive process     9      9/34
##                                                                                                                                                                                                geneID
## GO:0000003                                                                                                                                             SRC/ITGA2/GSK3A/ERCC1/PTEN/GATA3/ATM/EGFR/MSH6
## GO:0002376                                                                                                    SRC/MAPK1/ITGA2/YWHAE/TSC1/MAP2K1/ERCC1/G6PD/RBM15/GATA3/ATM/XBP1/GAPDH/MSH6/TFRC/PREX1
## GO:0008152                       AKT1S1/SRC/MAPK1/ITGA2/YWHAE/TSC1/PDCD4/GSK3A/RAB11B/KEAP1/XRCC1/PDK1/MAP2K1/FOXM1/ERCC1/G6PD/ASNS/RBM15/PTEN/GATA3/ATM/EGFR/IRS1/VHL/XBP1/GAPDH/MSH6/NF2/TFRC/PREX1
## GO:0009987 AKT1S1/SRC/MAPK1/VASP/ITGA2/YWHAE/TSC1/ANLN/PDCD4/GSK3A/RAB11B/KEAP1/XRCC1/PDK1/MAP2K1/FOXM1/ERCC1/G6PD/ASNS/RBM15/PTEN/GATA3/PEA15/ATM/EGFR/IRS1/VHL/XBP1/GAPDH/MSH6/MYH11/NF2/TFRC/PREX1
## GO:0016032                                                                                                                                                                      ITGA2/GSK3A/EGFR/TFRC
## GO:0022414                                                                                                                                             SRC/ITGA2/GSK3A/ERCC1/PTEN/GATA3/ATM/EGFR/MSH6
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    20     20/34
## GO:0044423 GO:0044423           virion component     0      0/34
## GO:0110165 GO:0110165 cellular anatomical entity    34     34/34
##                                                                                                                                                                                                geneID
## GO:0032991                                                                            AKT1S1/ITGA2/TSC1/GSK3A/KEAP1/XRCC1/PDK1/FOXM1/ERCC1/RBM15/GATA3/PEA15/ATM/EGFR/IRS1/XBP1/GAPDH/MSH6/MYH11/TFRC
## GO:0044423                                                                                                                                                                                           
## GO:0110165 AKT1S1/SRC/MAPK1/VASP/ITGA2/YWHAE/TSC1/ANLN/PDCD4/GSK3A/RAB11B/KEAP1/XRCC1/PDK1/MAP2K1/FOXM1/ERCC1/G6PD/ASNS/RBM15/PTEN/GATA3/PEA15/ATM/EGFR/IRS1/VHL/XBP1/GAPDH/MSH6/MYH11/NF2/TFRC/PREX1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/34
## GO:0003824 GO:0003824           catalytic activity    16     16/34
## GO:0005198 GO:0005198 structural molecule activity     1      1/34
## GO:0005215 GO:0005215         transporter activity     0      0/34
## GO:0005488 GO:0005488                      binding    34     34/34
## GO:0009055 GO:0009055   electron transfer activity     0      0/34
##                                                                                                                                                                                                             geneID
## GO:0003774                                                                                                                                                                                                        
## GO:0003824                                                                                                           MAPK14/AKT3/RAD51/BIRC2/ADAR/BRCA2/PCNA/ACACB/CDK1/XRCC1/TYMS/TUBA1B/EZH2/PARP1/INPP4B/ACVRL1
## GO:0005198                                                                                                                                                                                                  TUBA1B
## GO:0005215                                                                                                                                                                                                        
## GO:0005488 MAPK14/ERBB3/AKT3/CDH2/RAD51/BECN1/BIRC2/ITGA2/ADAR/BRCA2/PCNA/CTNNB1/ANLN/SHC1/STMN1/ACACB/CDK1/E2F1/XRCC1/TYMS/CCNB1/TUBA1B/NOTCH3/FOXM1/EZH2/CCNE2/ERRFI1/PARP1/RPTOR/CDKN2A/PEA15/INPP4B/ACVRL1/NF2
## GO:0009055                                                                                                                                                                                                        
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     9      9/34
## GO:0002376 GO:0002376 immune system process     9      9/34
## GO:0008152 GO:0008152     metabolic process    29     29/34
## GO:0009987 GO:0009987      cellular process    34     34/34
## GO:0016032 GO:0016032         viral process     4      4/34
## GO:0022414 GO:0022414  reproductive process     9      9/34
##                                                                                                                                                                                                             geneID
## GO:0000003                                                                                                                                                   RAD51/ITGA2/BRCA2/PCNA/CTNNB1/CDK1/CCNE2/ERRFI1/PARP1
## GO:0002376                                                                                                                                                   MAPK14/BECN1/BIRC2/ITGA2/ADAR/CTNNB1/EZH2/PARP1/RPTOR
## GO:0008152                              MAPK14/ERBB3/AKT3/RAD51/BECN1/BIRC2/ITGA2/ADAR/BRCA2/PCNA/CTNNB1/SHC1/ACACB/CDK1/E2F1/XRCC1/TYMS/CCNB1/NOTCH3/FOXM1/EZH2/CCNE2/ERRFI1/PARP1/RPTOR/CDKN2A/INPP4B/ACVRL1/NF2
## GO:0009987 MAPK14/ERBB3/AKT3/CDH2/RAD51/BECN1/BIRC2/ITGA2/ADAR/BRCA2/PCNA/CTNNB1/ANLN/SHC1/STMN1/ACACB/CDK1/E2F1/XRCC1/TYMS/CCNB1/TUBA1B/NOTCH3/FOXM1/EZH2/CCNE2/ERRFI1/PARP1/RPTOR/CDKN2A/PEA15/INPP4B/ACVRL1/NF2
## GO:0016032                                                                                                                                                                                   BECN1/ITGA2/ADAR/CDK1
## GO:0022414                                                                                                                                                   RAD51/ITGA2/BRCA2/PCNA/CTNNB1/CDK1/CCNE2/ERRFI1/PARP1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    25     25/34
## GO:0044423 GO:0044423           virion component     0      0/34
## GO:0110165 GO:0110165 cellular anatomical entity    34     34/34
##                                                                                                                                                                                                             geneID
## GO:0032991                                                      ERBB3/CDH2/RAD51/BECN1/BIRC2/ITGA2/ADAR/BRCA2/PCNA/CTNNB1/SHC1/ACACB/CDK1/E2F1/XRCC1/CCNB1/NOTCH3/FOXM1/EZH2/CCNE2/PARP1/RPTOR/CDKN2A/PEA15/ACVRL1
## GO:0044423                                                                                                                                                                                                        
## GO:0110165 MAPK14/ERBB3/AKT3/CDH2/RAD51/BECN1/BIRC2/ITGA2/ADAR/BRCA2/PCNA/CTNNB1/ANLN/SHC1/STMN1/ACACB/CDK1/E2F1/XRCC1/TYMS/CCNB1/TUBA1B/NOTCH3/FOXM1/EZH2/CCNE2/ERRFI1/PARP1/RPTOR/CDKN2A/PEA15/INPP4B/ACVRL1/NF2
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/36
## GO:0003824 GO:0003824           catalytic activity    12     12/36
## GO:0005198 GO:0005198 structural molecule activity     3      3/36
## GO:0005215 GO:0005215         transporter activity     1      1/36
## GO:0005488 GO:0005488                      binding    34     34/36
## GO:0009055 GO:0009055   electron transfer activity     0      0/36
##                                                                                                                                                                                                    geneID
## GO:0003774                                                                                                                                                                                           MYH9
## GO:0003824                                                                                                                                AKT2/AXL/MAPK1/BIRC2/XRCC5/PTK2/LCK/RAB25/PARP1/CASP9/NAPSA/SYK
## GO:0005198                                                                                                                                                                              CLDN7/CTNNA1/KRT5
## GO:0005215                                                                                                                                                                                         KCNJ13
## GO:0005488 ERBB3/EIF4EBP1/AKT2/CLDN7/ESR1/GATA3/EIF4G1/AXL/MAPK1/BIRC2/XRCC5/LCN2/CDH3/PDCD4/PTK2/PRRT2/MS4A1/LCK/CTNNA1/TP63/NRG1/KRT5/MYH9/YWHAB/RAB25/BID/TFRC/ERRFI1/PARP1/CASP9/NAPSA/SYK/TFF1/MACC1
## GO:0009055                                                                                                                                                                                               
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/36
## GO:0002376 GO:0002376 immune system process    16     16/36
## GO:0008152 GO:0008152     metabolic process    28     28/36
## GO:0009987 GO:0009987      cellular process    35     35/36
## GO:0016032 GO:0016032         viral process     2      2/36
## GO:0022414 GO:0022414  reproductive process     8      8/36
##                                                                                                                                                                                                          geneID
## GO:0000003                                                                                                                                                         ESR1/GATA3/AXL/CTNNA1/TP63/MYH9/ERRFI1/PARP1
## GO:0002376                                                                                                                    ESR1/GATA3/AXL/MAPK1/BIRC2/XRCC5/LCN2/PTK2/MS4A1/LCK/MYH9/BID/TFRC/PARP1/SYK/CHGA
## GO:0008152                                           ERBB3/EIF4EBP1/AKT2/ESR1/GATA3/EIF4G1/AXL/MAPK1/BIRC2/XRCC5/LCN2/CDH3/PDCD4/PTK2/LCK/TP63/NRG1/MYH9/YWHAB/BID/TFRC/ERRFI1/PARP1/CASP9/NAPSA/SYK/TFF1/MACC1
## GO:0009987 ERBB3/EIF4EBP1/AKT2/CLDN7/ESR1/GATA3/EIF4G1/AXL/MAPK1/BIRC2/XRCC5/LCN2/CDH3/PDCD4/PTK2/PRRT2/MS4A1/LCK/CTNNA1/TP63/NRG1/KRT5/MYH9/YWHAB/RAB25/BID/TFRC/ERRFI1/PARP1/CASP9/SYK/TFF1/MACC1/CHGA/KCNJ13
## GO:0016032                                                                                                                                                                                             AXL/TFRC
## GO:0022414                                                                                                                                                         ESR1/GATA3/AXL/CTNNA1/TP63/MYH9/ERRFI1/PARP1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    16     16/36
## GO:0044423 GO:0044423           virion component     0      0/36
## GO:0110165 GO:0110165 cellular anatomical entity    36     36/36
##                                                                                                                                                                                                                geneID
## GO:0032991                                                                                                                  ERBB3/ESR1/GATA3/EIF4G1/AXL/BIRC2/XRCC5/CDH3/CTNNA1/TP63/MYH9/TFRC/PARP1/CASP9/SYK/KCNJ13
## GO:0044423                                                                                                                                                                                                           
## GO:0110165 ERBB3/EIF4EBP1/AKT2/CLDN7/ESR1/GATA3/EIF4G1/AXL/MAPK1/BIRC2/XRCC5/LCN2/CDH3/PDCD4/PTK2/PRRT2/MS4A1/LCK/CTNNA1/TP63/NRG1/KRT5/MYH9/YWHAB/RAB25/BID/TFRC/ERRFI1/PARP1/CASP9/NAPSA/SYK/TFF1/MACC1/CHGA/KCNJ13
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/44
## GO:0003824 GO:0003824           catalytic activity    19     19/44
## GO:0005198 GO:0005198 structural molecule activity     2      2/44
## GO:0005215 GO:0005215         transporter activity     1      1/44
## GO:0005488 GO:0005488                      binding    44     44/44
## GO:0009055 GO:0009055   electron transfer activity     0      0/44
##                                                                                                                                                                                                                                                                      geneID
## GO:0003774                                                                                                                                                                                                                                                             MYH9
## GO:0003824                                                                                                                                                    CASP3/ATM/XIAP/MAPK8/TUBA1B/INPP4B/MAPK1/FASN/CDKN1A/NRAS/ADAR/CCND1/PARP1/EEF2/MTOR/GSK3B/IGF1R/PRDX1/PRKAA1
## GO:0005198                                                                                                                                                                                                                                                    TUBA1B/CTNNA1
## GO:0005215                                                                                                                                                                                                                                                            IGF1R
## GO:0005488 CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/TUBA1B/YWHAZ/EIF4G1/YWHAE/ARID1A/NDRG1/INPP4B/TP53/AR/MAPK1/FASN/CDKN1A/STAT5A/NF2/NRAS/ADAR/PREX1/MYH9/CCND1/CDKN1B/BCL2L11/PARP1/ANXA7/CTNNA1/EEF2/MTOR/GSK3B/IGF1R/PRDX1/SERPINE1/PRKAA1/PXN/SRSF1/SYP/TFRC/WWTR1/YWHAB/MACC1
## GO:0009055                                                                                                                                                                                                                                                                 
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    11     11/44
## GO:0002376 GO:0002376 immune system process    21     21/44
## GO:0008152 GO:0008152     metabolic process    37     37/44
## GO:0009987 GO:0009987      cellular process    44     44/44
## GO:0016032 GO:0016032         viral process     4      4/44
## GO:0022414 GO:0022414  reproductive process    11     11/44
##                                                                                                                                                                                                                                                                      geneID
## GO:0000003                                                                                                                                                                                                   CASP3/ATM/SMAD4/AR/MYH9/CDKN1B/BCL2L11/PARP1/CTNNA1/MTOR/IGF1R
## GO:0002376                                                                                                                                     CASP3/ATM/XIAP/MAPK8/YWHAZ/YWHAE/ARID1A/NDRG1/TP53/MAPK1/CDKN1A/ADAR/PREX1/MYH9/BCL2L11/PARP1/MTOR/IGF1R/PRDX1/SERPINE1/TFRC
## GO:0008152                                          CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/YWHAZ/EIF4G1/YWHAE/ARID1A/INPP4B/TP53/AR/MAPK1/FASN/CDKN1A/STAT5A/NF2/ADAR/PREX1/MYH9/CCND1/CDKN1B/PARP1/ANXA7/EEF2/MTOR/GSK3B/IGF1R/PRDX1/SERPINE1/PRKAA1/SRSF1/TFRC/WWTR1/YWHAB/MACC1
## GO:0009987 CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/TUBA1B/YWHAZ/EIF4G1/YWHAE/ARID1A/NDRG1/INPP4B/TP53/AR/MAPK1/FASN/CDKN1A/STAT5A/NF2/NRAS/ADAR/PREX1/MYH9/CCND1/CDKN1B/BCL2L11/PARP1/ANXA7/CTNNA1/EEF2/MTOR/GSK3B/IGF1R/PRDX1/SERPINE1/PRKAA1/PXN/SRSF1/SYP/TFRC/WWTR1/YWHAB/MACC1
## GO:0016032                                                                                                                                                                                                                                             TP53/ADAR/GSK3B/TFRC
## GO:0022414                                                                                                                                                                                                   CASP3/ATM/SMAD4/AR/MYH9/CDKN1B/BCL2L11/PARP1/CTNNA1/MTOR/IGF1R
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    27     27/44
## GO:0044423 GO:0044423           virion component     0      0/44
## GO:0110165 GO:0110165 cellular anatomical entity    44     44/44
##                                                                                                                                                                                                                                                                      geneID
## GO:0032991                                                                                                  CASP3/CDH1/ATM/SMAD4/EIF4G1/ARID1A/TP53/AR/CDKN1A/STAT5A/ADAR/MYH9/CCND1/CDKN1B/BCL2L11/PARP1/CTNNA1/EEF2/MTOR/GSK3B/IGF1R/SERPINE1/PRKAA1/PXN/SRSF1/TFRC/WWTR1
## GO:0044423                                                                                                                                                                                                                                                                 
## GO:0110165 CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/TUBA1B/YWHAZ/EIF4G1/YWHAE/ARID1A/NDRG1/INPP4B/TP53/AR/MAPK1/FASN/CDKN1A/STAT5A/NF2/NRAS/ADAR/PREX1/MYH9/CCND1/CDKN1B/BCL2L11/PARP1/ANXA7/CTNNA1/EEF2/MTOR/GSK3B/IGF1R/PRDX1/SERPINE1/PRKAA1/PXN/SRSF1/SYP/TFRC/WWTR1/YWHAB/MACC1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/72
## GO:0003824 GO:0003824           catalytic activity    39     39/72
## GO:0005198 GO:0005198 structural molecule activity     2      2/72
## GO:0005215 GO:0005215         transporter activity     1      1/72
## GO:0005488 GO:0005488                      binding    71     71/72
## GO:0009055 GO:0009055   electron transfer activity     0      0/72
##                                                                                                                                                                                                                                                                                                                                                                                                                                     geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                                                                                                            MYH9
## GO:0003824                                                                                                                                                                                            CCNE1/PTEN/PIK3R1/CDK1/IDH3A/RAD51/RPS6KB1/TUBA1B/MAPK14/NRAS/ADAR/CCND1/CDKN1A/EGFR/ARAF/MSH2/EZH2/MAPK9/BRCA2/PTGS2/TYMS/AKT2/MAP2K1/AKT3/BIRC2/EEF2/GSK3B/IGF1R/PCNA/PRKAA1/PRKCA/MAPK3/MAPK8/TGM2/RAB11A/INPP4B/FASN/RAB11B/BRAF
## GO:0005198                                                                                                                                                                                                                                                                                                                                                                                                                   TUBA1B/CTNNA1
## GO:0005215                                                                                                                                                                                                                                                                                                                                                                                                                           IGF1R
## GO:0005488 CCNE1/PTEN/CAV1/PIK3R1/CDK1/IDH3A/ITGA2/RAD51/RPS6KB1/SRSF1/PEA15/TUBA1B/MAPK14/E2F1/NRAS/ADAR/MYH9/CCND1/CDKN1A/IRS1/MYC/EGFR/TP63/ARAF/JUN/MSH2/EZH2/MAPK9/PIK3R2/BRCA2/PTGS2/TYMS/TP53/AKT2/MAP2K1/NFKB1/ERRFI1/AKT3/BIRC2/CCNB1/CTNNA1/CTNNB1/EEF2/EIF4G1/FOXM1/GSK3B/IGF1R/IGFBP2/SMAD4/SERPINE1/PCNA/PRKAA1/PRKCA/MAPK3/MAPK8/PXN/TFRC/TGM2/ARID1A/BECN1/RAB11A/SQSTM1/ANLN/INPP4B/YWHAB/FASN/RAB11B/BRAF/PRRT2/MACC1/NF2
## GO:0009055                                                                                                                                                                                                                                                                                                                                                                                                                                
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    19     19/72
## GO:0002376 GO:0002376 immune system process    30     30/72
## GO:0008152 GO:0008152     metabolic process    62     62/72
## GO:0009987 GO:0009987      cellular process    72     72/72
## GO:0016032 GO:0016032         viral process    10     10/72
## GO:0022414 GO:0022414  reproductive process    19     19/72
##                                                                                                                                                                                                                                                                                                                                                                                                                                          geneID
## GO:0000003                                                                                                                                                                                                                                                                                                                     CCNE1/PTEN/CDK1/ITGA2/RAD51/RPS6KB1/MYH9/EGFR/TP63/MSH2/BRCA2/PTGS2/ERRFI1/CTNNA1/CTNNB1/IGF1R/IGFBP2/SMAD4/PCNA
## GO:0002376                                                                                                                                                                                                                                               CAV1/PIK3R1/ITGA2/RPS6KB1/CHGA/MAPK14/ADAR/MYH9/CDKN1A/MYC/MSH2/EZH2/MAPK9/PIK3R2/TP53/MAP2K1/NFKB1/BIRC2/CTNNB1/IGF1R/IGFBP2/SERPINE1/PRKCA/MAPK3/MAPK8/TFRC/ARID1A/BECN1/SQSTM1/BRAF
## GO:0008152                                                            CCNE1/PTEN/CAV1/PIK3R1/CDK1/IDH3A/ITGA2/RAD51/RPS6KB1/SRSF1/MAPK14/E2F1/ADAR/MYH9/CCND1/CDKN1A/IRS1/MYC/EGFR/TP63/ARAF/JUN/MSH2/EZH2/MAPK9/PIK3R2/BRCA2/PTGS2/TYMS/TP53/AKT2/MAP2K1/NFKB1/ERRFI1/AKT3/BIRC2/CCNB1/CTNNB1/EEF2/EIF4G1/FOXM1/GSK3B/IGF1R/SMAD4/SERPINE1/PCNA/PRKAA1/PRKCA/MAPK3/MAPK8/TFRC/TGM2/ARID1A/BECN1/SQSTM1/INPP4B/YWHAB/FASN/RAB11B/BRAF/MACC1/NF2
## GO:0009987 CCNE1/PTEN/CAV1/PIK3R1/CDK1/IDH3A/ITGA2/RAD51/RPS6KB1/SRSF1/PEA15/TUBA1B/CHGA/MAPK14/E2F1/NRAS/ADAR/MYH9/CCND1/CDKN1A/IRS1/MYC/EGFR/TP63/ARAF/JUN/MSH2/EZH2/MAPK9/PIK3R2/BRCA2/PTGS2/TYMS/TP53/AKT2/MAP2K1/NFKB1/ERRFI1/AKT3/BIRC2/CCNB1/CTNNA1/CTNNB1/EEF2/EIF4G1/FOXM1/GSK3B/IGF1R/IGFBP2/SMAD4/SERPINE1/PCNA/PRKAA1/PRKCA/MAPK3/MAPK8/PXN/TFRC/TGM2/ARID1A/BECN1/RAB11A/SQSTM1/ANLN/INPP4B/YWHAB/FASN/RAB11B/BRAF/PRRT2/MACC1/NF2
## GO:0016032                                                                                                                                                                                                                                                                                                                                                                                  CAV1/CDK1/ITGA2/ADAR/EGFR/JUN/TP53/GSK3B/TFRC/BECN1
## GO:0022414                                                                                                                                                                                                                                                                                                                     CCNE1/PTEN/CDK1/ITGA2/RAD51/RPS6KB1/MYH9/EGFR/TP63/MSH2/BRCA2/PTGS2/ERRFI1/CTNNA1/CTNNB1/IGF1R/IGFBP2/SMAD4/PCNA
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    46     46/72
## GO:0044423 GO:0044423           virion component     0      0/72
## GO:0110165 GO:0110165 cellular anatomical entity    72     72/72
##                                                                                                                                                                                                                                                                                                                                                                                                                                          geneID
## GO:0032991                                                                                                                                                           CCNE1/CAV1/PIK3R1/CDK1/IDH3A/ITGA2/RAD51/SRSF1/PEA15/E2F1/ADAR/MYH9/CCND1/CDKN1A/IRS1/MYC/EGFR/TP63/JUN/MSH2/EZH2/PIK3R2/BRCA2/PTGS2/TP53/NFKB1/BIRC2/CCNB1/CTNNA1/CTNNB1/EEF2/EIF4G1/FOXM1/GSK3B/IGF1R/SMAD4/SERPINE1/PCNA/PRKAA1/PRKCA/PXN/TFRC/TGM2/ARID1A/BECN1/RAB11A
## GO:0044423                                                                                                                                                                                                                                                                                                                                                                                                                                     
## GO:0110165 CCNE1/PTEN/CAV1/PIK3R1/CDK1/IDH3A/ITGA2/RAD51/RPS6KB1/SRSF1/PEA15/TUBA1B/CHGA/MAPK14/E2F1/NRAS/ADAR/MYH9/CCND1/CDKN1A/IRS1/MYC/EGFR/TP63/ARAF/JUN/MSH2/EZH2/MAPK9/PIK3R2/BRCA2/PTGS2/TYMS/TP53/AKT2/MAP2K1/NFKB1/ERRFI1/AKT3/BIRC2/CCNB1/CTNNA1/CTNNB1/EEF2/EIF4G1/FOXM1/GSK3B/IGF1R/IGFBP2/SMAD4/SERPINE1/PCNA/PRKAA1/PRKCA/MAPK3/MAPK8/PXN/TFRC/TGM2/ARID1A/BECN1/RAB11A/SQSTM1/ANLN/INPP4B/YWHAB/FASN/RAB11B/BRAF/PRRT2/MACC1/NF2
barplot(ggo_MF[[1]], title = "groupGO, Molecular Function, Factor 1 of 1")

barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, Factor 1 of 2")

barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, Factor 2 of 2")

barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, Factor 1 of 3")

barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, Factor 2 of 3")

barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, Factor 3 of 3")

barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, Factor 1 of 5")

barplot(ggo_MF[[8]], title = "groupGO, Molecular Function, Factor 2 of 5")

barplot(ggo_MF[[9]], title = "groupGO, Molecular Function, Factor 3 of 5")

barplot(ggo_MF[[10]], title = "groupGO, Molecular Function, Factor 4 of 5")

barplot(ggo_MF[[11]], title = "groupGO, Molecular Function, Factor 5 of 5")

barplot(ggo_MF[[12]], title = "groupGO, Molecular Function, Factor 1 of 10")

barplot(ggo_MF[[13]], title = "groupGO, Molecular Function, Factor 2 of 10")

barplot(ggo_MF[[14]], title = "groupGO, Molecular Function, Factor 3 of 10")

barplot(ggo_MF[[15]], title = "groupGO, Molecular Function, Factor 4 of 10")

barplot(ggo_MF[[16]], title = "groupGO, Molecular Function, Factor 5 of 10")

barplot(ggo_MF[[17]], title = "groupGO, Molecular Function, Factor 6 of 10")

barplot(ggo_MF[[18]], title = "groupGO, Molecular Function, Factor 7 of 10")

barplot(ggo_MF[[19]], title = "groupGO, Molecular Function, Factor 8 of 10")

barplot(ggo_MF[[20]], title = "groupGO, Molecular Function, Factor 9 of 10")

barplot(ggo_MF[[21]], title = "groupGO, Molecular Function, Factor 10 of 10")

barplot(ggo_BP[[1]], title = "groupGO, Biological Process, Factor 1 of 1")

barplot(ggo_BP[[2]], title = "groupGO, Biological Process, Factor 1 of 2")

barplot(ggo_BP[[3]], title = "groupGO, Biological Process, Factor 2 of 2")

barplot(ggo_BP[[4]], title = "groupGO, Biological Process, Factor 1 of 3")

barplot(ggo_BP[[5]], title = "groupGO, Biological Process, Factor 2 of 3")

barplot(ggo_BP[[6]], title = "groupGO, Biological Process, Factor 3 of 3")

barplot(ggo_BP[[7]], title = "groupGO, Biological Process, Factor 1 of 5")

barplot(ggo_BP[[8]], title = "groupGO, Biological Process, Factor 2 of 5")

barplot(ggo_BP[[9]], title = "groupGO, Biological Process, Factor 3 of 5")

barplot(ggo_BP[[10]], title = "groupGO, Biological Process, Factor 4 of 5")

barplot(ggo_BP[[11]], title = "groupGO, Biological Process, Factor 5 of 5")

barplot(ggo_BP[[12]], title = "groupGO, Biological Process, Factor 1 of 10")

barplot(ggo_BP[[13]], title = "groupGO, Biological Process, Factor 2 of 10")

barplot(ggo_BP[[14]], title = "groupGO, Biological Process, Factor 3 of 10")

barplot(ggo_BP[[15]], title = "groupGO, Biological Process, Factor 4 of 10")

barplot(ggo_BP[[16]], title = "groupGO, Biological Process, Factor 5 of 10")

barplot(ggo_BP[[17]], title = "groupGO, Biological Process, Factor 6 of 10")

barplot(ggo_BP[[18]], title = "groupGO, Biological Process, Factor 7 of 10")

barplot(ggo_BP[[19]], title = "groupGO, Biological Process, Factor 8 of 10")

barplot(ggo_BP[[20]], title = "groupGO, Biological Process, Factor 9 of 10")

barplot(ggo_BP[[21]], title = "groupGO, Biological Process, Factor 10 of 10")

barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, Factor 1 of 1")

barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, Factor 1 of 2")

barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, Factor 2 of 2")

barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, Factor 1 of 3")

barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, Factor 2 of 3")

barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, Factor 3 of 3")

barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, Factor 1 of 5")

barplot(ggo_CC[[8]], title = "groupGO, Cellular Component, Factor 2 of 5")

barplot(ggo_CC[[9]], title = "groupGO, Cellular Component, Factor 3 of 5")

barplot(ggo_CC[[10]], title = "groupGO, Cellular Component, Factor 4 of 5")

barplot(ggo_CC[[11]], title = "groupGO, Cellular Component, Factor 5 of 5")

barplot(ggo_CC[[12]], title = "groupGO, Cellular Component, Factor 1 of 10")

barplot(ggo_CC[[13]], title = "groupGO, Cellular Component, Factor 2 of 10")

barplot(ggo_CC[[14]], title = "groupGO, Cellular Component, Factor 3 of 10")

barplot(ggo_CC[[15]], title = "groupGO, Cellular Component, Factor 4 of 10")

barplot(ggo_CC[[16]], title = "groupGO, Cellular Component, Factor 5 of 10")

barplot(ggo_CC[[17]], title = "groupGO, Cellular Component, Factor 6 of 10")

barplot(ggo_CC[[18]], title = "groupGO, Cellular Component, Factor 7 of 10")

barplot(ggo_CC[[19]], title = "groupGO, Cellular Component, Factor 8 of 10")

barplot(ggo_CC[[20]], title = "groupGO, Cellular Component, Factor 9 of 10")

barplot(ggo_CC[[21]], title = "groupGO, Cellular Component, Factor 10 of 10")

B. GO Over-Representation

ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]
  ego_MF[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "MF",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_BP[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "BP",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_CC[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "CC",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16
## [1] 17
## [1] 18
## [1] 19
## [1] 20
## [1] 21
for(z in 1:length(geneNames)){
  print(head(ego_MF[[z]]))
  print(head(ego_BP[[z]]))
  print(head(ego_CC[[z]]))
}
##                    ID                              Description GeneRatio
## GO:0120283 GO:0120283  protein serine/threonine kinase binding      2/23
## GO:0106310 GO:0106310           protein serine kinase activity      5/23
## GO:0004674 GO:0004674 protein serine/threonine kinase activity      5/23
## GO:0004707 GO:0004707                      MAP kinase activity      2/23
## GO:0070064 GO:0070064              proline-rich region binding      2/23
## GO:0042826 GO:0042826              histone deacetylase binding      3/23
##              BgRatio       pvalue    p.adjust      qvalue
## GO:0120283   7/18522 3.085855e-05 0.005523681 0.002273788
## GO:0106310 363/18522 7.075911e-05 0.006332941 0.002606915
## GO:0004674 427/18522 1.518718e-04 0.007100610 0.002922921
## GO:0004707  16/18522 1.751391e-04 0.007100610 0.002922921
## GO:0070064  17/18522 1.983411e-04 0.007100610 0.002922921
## GO:0042826 128/18522 5.160029e-04 0.015394085 0.006336877
##                               geneID Count
## GO:0120283                MAPK8/XIAP     2
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004707               MAPK8/MAPK1     2
## GO:0070064                CCND1/YAP1     2
## GO:0042826        HSPA1A/MAPK8/CCND1     3
##                    ID                                 Description GeneRatio
## GO:0010631 GO:0010631                   epithelial cell migration      9/23
## GO:0090132 GO:0090132                        epithelium migration      9/23
## GO:0090130 GO:0090130                            tissue migration      9/23
## GO:0001667 GO:0001667               ameboidal-type cell migration      9/23
## GO:0071214 GO:0071214       cellular response to abiotic stimulus      8/23
## GO:0104004 GO:0104004 cellular response to environmental stimulus      8/23
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0010631 375/18888 2.784961e-10 2.143530e-07 8.314100e-08
## GO:0090132 378/18888 2.988249e-10 2.143530e-07 8.314100e-08
## GO:0090130 383/18888 3.356258e-10 2.143530e-07 8.314100e-08
## GO:0001667 498/18888 3.370825e-09 1.092718e-06 4.238319e-07
## GO:0071214 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## GO:0104004 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
##                                                     geneID Count
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0001667 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0071214     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
## GO:0104004     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
##                    ID                  Description GeneRatio   BgRatio
## GO:0005925 GO:0005925               focal adhesion      6/23 421/19894
## GO:0030055 GO:0030055      cell-substrate junction      6/23 431/19894
## GO:0005826 GO:0005826  actomyosin contractile ring      2/23   4/19894
## GO:0070938 GO:0070938             contractile ring      2/23  10/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane      4/23 219/19894
## GO:0031968 GO:0031968     organelle outer membrane      4/23 248/19894
##                  pvalue     p.adjust       qvalue
## GO:0005925 6.447048e-06 0.0003166418 0.0001720295
## GO:0030055 7.373490e-06 0.0003166418 0.0001720295
## GO:0005826 7.660689e-06 0.0003166418 0.0001720295
## GO:0070938 5.721303e-05 0.0017736039 0.0009635879
## GO:0005741 1.073470e-04 0.0026622052 0.0014463593
## GO:0031968 1.732117e-04 0.0031642699 0.0017191279
##                                       geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1     6
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1     6
## GO:0005826                         MYH9/ANLN     2
## GO:0070938                         MYH9/ANLN     2
## GO:0005741             MTOR/FOXO3/CASP8/KRAS     4
## GO:0031968             MTOR/FOXO3/CASP8/KRAS     4
##                    ID                               Description GeneRatio
## GO:0032143 GO:0032143          single thymine insertion binding      2/27
## GO:0032137 GO:0032137           guanine/thymine mispair binding      2/27
## GO:0032142 GO:0032142          single guanine insertion binding      2/27
## GO:0032138 GO:0032138 single base insertion or deletion binding      2/27
## GO:0097718 GO:0097718        disordered domain specific binding      3/27
## GO:0032135 GO:0032135         DNA insertion or deletion binding      2/27
##             BgRatio       pvalue     p.adjust       qvalue          geneID
## GO:0032143  2/18522 2.046373e-06 0.0003864164 0.0001743232       MSH6/MSH2
## GO:0032137  3/18522 6.133594e-06 0.0003864164 0.0001743232       MSH6/MSH2
## GO:0032142  3/18522 6.133594e-06 0.0003864164 0.0001743232       MSH6/MSH2
## GO:0032138  4/18522 1.225615e-05 0.0005035163 0.0002271502       MSH6/MSH2
## GO:0097718 32/18522 1.332054e-05 0.0005035163 0.0002271502 RB1/NCOA3/GAPDH
## GO:0032135  6/18522 3.058526e-05 0.0008258020 0.0003725423       MSH6/MSH2
##            Count
## GO:0032143     2
## GO:0032137     2
## GO:0032142     2
## GO:0032138     2
## GO:0097718     3
## GO:0032135     2
##                    ID
## GO:0051402 GO:0051402
## GO:0045785 GO:0045785
## GO:0008630 GO:0008630
## GO:0043254 GO:0043254
## GO:0030099 GO:0030099
## GO:0002562 GO:0002562
##                                                                                             Description
## GO:0051402                                                                     neuron apoptotic process
## GO:0045785                                                         positive regulation of cell adhesion
## GO:0008630                              intrinsic apoptotic signaling pathway in response to DNA damage
## GO:0043254                                            regulation of protein-containing complex assembly
## GO:0030099                                                                 myeloid cell differentiation
## GO:0002562 somatic diversification of immune receptors via germline recombination within a single locus
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0051402      7/27 292/18888 1.338203e-07 0.0001484232 8.674955e-05
## GO:0045785      8/27 485/18888 2.577809e-07 0.0001484232 8.674955e-05
## GO:0008630      5/27 102/18888 3.056072e-07 0.0001484232 8.674955e-05
## GO:0043254      7/27 418/18888 1.497283e-06 0.0005244227 3.065115e-04
## GO:0030099      7/27 439/18888 2.073983e-06 0.0005244227 3.065115e-04
## GO:0002562      4/27  70/18888 2.846143e-06 0.0005244227 3.065115e-04
##                                                 geneID Count
## GO:0051402            RB1/XIAP/BID/G6PD/ATM/GAPDH/MSH2     7
## GO:0045785 ETS1/ARID1A/IGFBP2/ATM/TSC1/XBP1/TFRC/PREX1     8
## GO:0008630                     BID/ATM/BRCA2/MSH6/MSH2     5
## GO:0043254          RB1/MAPK8/BID/STMN1/ATM/TFRC/PREX1     7
## GO:0030099          RB1/ETS1/GAB2/G6PD/RBM15/FASN/TFRC     7
## GO:0002562                          ATM/MSH6/TFRC/MSH2     4
##                    ID             Description GeneRatio   BgRatio       pvalue
## GO:0032301 GO:0032301       MutSalpha complex      2/27   2/19894 1.773841e-06
## GO:0032300 GO:0032300 mismatch repair complex      2/27  11/19894 9.682824e-05
## GO:1990391 GO:1990391      DNA repair complex      2/27  22/19894 4.029496e-04
## GO:0042470 GO:0042470              melanosome      3/27 112/19894 4.604156e-04
## GO:0048770 GO:0048770         pigment granule      3/27 112/19894 4.604156e-04
## GO:0016514 GO:0016514         SWI/SNF complex      2/27  30/19894 7.537380e-04
##               p.adjust       qvalue          geneID Count
## GO:0032301 0.000200444 0.0001456417       MSH6/MSH2     2
## GO:0032300 0.005470795 0.0039750539       MSH6/MSH2     2
## GO:1990391 0.010405392 0.0075605085       ATM/BRCA2     2
## GO:0042470 0.010405392 0.0075605085 FASN/PRDX1/TFRC     3
## GO:0048770 0.010405392 0.0075605085 FASN/PRDX1/TFRC     3
## GO:0016514 0.014195400 0.0103143099      RB1/ARID1A     2
##                    ID                              Description GeneRatio
## GO:0120283 GO:0120283  protein serine/threonine kinase binding      2/23
## GO:0106310 GO:0106310           protein serine kinase activity      5/23
## GO:0004674 GO:0004674 protein serine/threonine kinase activity      5/23
## GO:0004707 GO:0004707                      MAP kinase activity      2/23
## GO:0070064 GO:0070064              proline-rich region binding      2/23
## GO:0042826 GO:0042826              histone deacetylase binding      3/23
##              BgRatio       pvalue    p.adjust      qvalue
## GO:0120283   7/18522 3.085855e-05 0.005523681 0.002273788
## GO:0106310 363/18522 7.075911e-05 0.006332941 0.002606915
## GO:0004674 427/18522 1.518718e-04 0.007100610 0.002922921
## GO:0004707  16/18522 1.751391e-04 0.007100610 0.002922921
## GO:0070064  17/18522 1.983411e-04 0.007100610 0.002922921
## GO:0042826 128/18522 5.160029e-04 0.015394085 0.006336877
##                               geneID Count
## GO:0120283                MAPK8/XIAP     2
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004707               MAPK8/MAPK1     2
## GO:0070064                CCND1/YAP1     2
## GO:0042826        HSPA1A/MAPK8/CCND1     3
##                    ID                                 Description GeneRatio
## GO:0010631 GO:0010631                   epithelial cell migration      9/23
## GO:0090132 GO:0090132                        epithelium migration      9/23
## GO:0090130 GO:0090130                            tissue migration      9/23
## GO:0001667 GO:0001667               ameboidal-type cell migration      9/23
## GO:0071214 GO:0071214       cellular response to abiotic stimulus      8/23
## GO:0104004 GO:0104004 cellular response to environmental stimulus      8/23
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0010631 375/18888 2.784961e-10 2.143530e-07 8.314100e-08
## GO:0090132 378/18888 2.988249e-10 2.143530e-07 8.314100e-08
## GO:0090130 383/18888 3.356258e-10 2.143530e-07 8.314100e-08
## GO:0001667 498/18888 3.370825e-09 1.092718e-06 4.238319e-07
## GO:0071214 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## GO:0104004 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
##                                                     geneID Count
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0001667 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0071214     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
## GO:0104004     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
##                    ID                  Description GeneRatio   BgRatio
## GO:0005925 GO:0005925               focal adhesion      6/23 421/19894
## GO:0030055 GO:0030055      cell-substrate junction      6/23 431/19894
## GO:0005826 GO:0005826  actomyosin contractile ring      2/23   4/19894
## GO:0070938 GO:0070938             contractile ring      2/23  10/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane      4/23 219/19894
## GO:0031968 GO:0031968     organelle outer membrane      4/23 248/19894
##                  pvalue     p.adjust       qvalue
## GO:0005925 6.447048e-06 0.0003166418 0.0001720295
## GO:0030055 7.373490e-06 0.0003166418 0.0001720295
## GO:0005826 7.660689e-06 0.0003166418 0.0001720295
## GO:0070938 5.721303e-05 0.0017736039 0.0009635879
## GO:0005741 1.073470e-04 0.0026622052 0.0014463593
## GO:0031968 1.732117e-04 0.0031642699 0.0017191279
##                                       geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1     6
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1     6
## GO:0005826                         MYH9/ANLN     2
## GO:0070938                         MYH9/ANLN     2
## GO:0005741             MTOR/FOXO3/CASP8/KRAS     4
## GO:0031968             MTOR/FOXO3/CASP8/KRAS     4
##                    ID                              Description GeneRatio
## GO:0120283 GO:0120283  protein serine/threonine kinase binding      2/23
## GO:0106310 GO:0106310           protein serine kinase activity      5/23
## GO:0004674 GO:0004674 protein serine/threonine kinase activity      5/23
## GO:0004707 GO:0004707                      MAP kinase activity      2/23
## GO:0070064 GO:0070064              proline-rich region binding      2/23
## GO:0042826 GO:0042826              histone deacetylase binding      3/23
##              BgRatio       pvalue    p.adjust      qvalue
## GO:0120283   7/18522 3.085855e-05 0.005523681 0.002273788
## GO:0106310 363/18522 7.075911e-05 0.006332941 0.002606915
## GO:0004674 427/18522 1.518718e-04 0.007100610 0.002922921
## GO:0004707  16/18522 1.751391e-04 0.007100610 0.002922921
## GO:0070064  17/18522 1.983411e-04 0.007100610 0.002922921
## GO:0042826 128/18522 5.160029e-04 0.015394085 0.006336877
##                               geneID Count
## GO:0120283                MAPK8/XIAP     2
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004707               MAPK8/MAPK1     2
## GO:0070064                CCND1/YAP1     2
## GO:0042826        HSPA1A/MAPK8/CCND1     3
##                    ID                                 Description GeneRatio
## GO:0010631 GO:0010631                   epithelial cell migration      9/23
## GO:0090132 GO:0090132                        epithelium migration      9/23
## GO:0090130 GO:0090130                            tissue migration      9/23
## GO:0001667 GO:0001667               ameboidal-type cell migration      9/23
## GO:0071214 GO:0071214       cellular response to abiotic stimulus      8/23
## GO:0104004 GO:0104004 cellular response to environmental stimulus      8/23
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0010631 375/18888 2.784961e-10 2.143530e-07 8.314100e-08
## GO:0090132 378/18888 2.988249e-10 2.143530e-07 8.314100e-08
## GO:0090130 383/18888 3.356258e-10 2.143530e-07 8.314100e-08
## GO:0001667 498/18888 3.370825e-09 1.092718e-06 4.238319e-07
## GO:0071214 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## GO:0104004 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
##                                                     geneID Count
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0001667 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0071214     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
## GO:0104004     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
##                    ID                  Description GeneRatio   BgRatio
## GO:0005925 GO:0005925               focal adhesion      6/23 421/19894
## GO:0030055 GO:0030055      cell-substrate junction      6/23 431/19894
## GO:0005826 GO:0005826  actomyosin contractile ring      2/23   4/19894
## GO:0070938 GO:0070938             contractile ring      2/23  10/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane      4/23 219/19894
## GO:0031968 GO:0031968     organelle outer membrane      4/23 248/19894
##                  pvalue     p.adjust       qvalue
## GO:0005925 6.447048e-06 0.0003166418 0.0001720295
## GO:0030055 7.373490e-06 0.0003166418 0.0001720295
## GO:0005826 7.660689e-06 0.0003166418 0.0001720295
## GO:0070938 5.721303e-05 0.0017736039 0.0009635879
## GO:0005741 1.073470e-04 0.0026622052 0.0014463593
## GO:0031968 1.732117e-04 0.0031642699 0.0017191279
##                                       geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1     6
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1     6
## GO:0005826                         MYH9/ANLN     2
## GO:0070938                         MYH9/ANLN     2
## GO:0005741             MTOR/FOXO3/CASP8/KRAS     4
## GO:0031968             MTOR/FOXO3/CASP8/KRAS     4
##                    ID
## GO:0140297 GO:0140297
## GO:0120283 GO:0120283
## GO:0031625 GO:0031625
## GO:0044389 GO:0044389
## GO:0140311 GO:0140311
## GO:0061629 GO:0061629
##                                                                    Description
## GO:0140297                            DNA-binding transcription factor binding
## GO:0120283                             protein serine/threonine kinase binding
## GO:0031625                                    ubiquitin protein ligase binding
## GO:0044389                               ubiquitin-like protein ligase binding
## GO:0140311                                       protein sequestering activity
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0140297      6/20 478/18522 8.157340e-06 0.001231758 0.0005495471
## GO:0120283      2/20   7/18522 2.318693e-05 0.001750613 0.0007810334
## GO:0031625      4/20 305/18522 2.836004e-04 0.011142865 0.0049713724
## GO:0044389      4/20 324/18522 3.568288e-04 0.011142865 0.0049713724
## GO:0140311      2/20  29/18522 4.419377e-04 0.011142865 0.0049713724
## GO:0061629      4/20 343/18522 4.427629e-04 0.011142865 0.0049713724
##                                     geneID Count
## GO:0140297 RB1/ETS1/ARID1A/YWHAZ/NCOA3/VHL     6
## GO:0120283                      XIAP/MAPK8     2
## GO:0031625            RB1/BID/YWHAZ/CDKN1A     4
## GO:0044389            RB1/BID/YWHAZ/CDKN1A     4
## GO:0140311                    YWHAZ/CDKN1A     2
## GO:0061629           RB1/ETS1/ARID1A/NCOA3     4
##                    ID
## GO:2000045 GO:2000045
## GO:1902806 GO:1902806
## GO:0000082 GO:0000082
## GO:0044843 GO:0044843
## GO:2000134 GO:2000134
## GO:1902807 GO:1902807
##                                                             Description
## GO:2000045          regulation of G1/S transition of mitotic cell cycle
## GO:1902806               regulation of cell cycle G1/S phase transition
## GO:0000082                        G1/S transition of mitotic cell cycle
## GO:0044843                             cell cycle G1/S phase transition
## GO:2000134 negative regulation of G1/S transition of mitotic cell cycle
## GO:1902807      negative regulation of cell cycle G1/S phase transition
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:2000045      7/20 185/18888 5.372413e-10 7.220523e-07 3.472275e-07
## GO:1902806      7/20 211/18888 1.346798e-09 9.050483e-07 4.352284e-07
## GO:0000082      7/20 234/18888 2.767587e-09 1.239879e-06 5.962451e-07
## GO:0044843      7/20 262/18888 6.061003e-09 2.036497e-06 9.793305e-07
## GO:2000134      5/20  85/18888 2.408730e-08 6.474667e-06 3.113601e-06
## GO:1902807      5/20  94/18888 4.006836e-08 8.975312e-06 4.316135e-06
##                                          geneID Count
## GO:2000045 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A     7
## GO:1902806 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A     7
## GO:0000082 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A     7
## GO:0044843 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A     7
## GO:2000134            RB1/PTEN/ATM/CCND1/CDKN1A     5
## GO:1902807            RB1/PTEN/ATM/CCND1/CDKN1A     5
##                    ID                                        Description
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:1902554 GO:1902554            serine/threonine protein kinase complex
## GO:0016514 GO:0016514                                    SWI/SNF complex
## GO:1902911 GO:1902911                             protein kinase complex
## GO:0005925 GO:0005925                                     focal adhesion
## GO:0030055 GO:0030055                            cell-substrate junction
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0000307      3/20  56/19894 2.328041e-05 0.002165078 0.001151768
## GO:1902554      3/20 136/19894 3.271542e-04 0.010135391 0.005391776
## GO:0016514      2/20  30/19894 4.106920e-04 0.010135391 0.005391776
## GO:1902911      3/20 150/19894 4.359308e-04 0.010135391 0.005391776
## GO:0005925      4/20 421/19894 7.320323e-04 0.012387254 0.006589711
## GO:0030055      4/20 431/19894 7.991777e-04 0.012387254 0.006589711
##                           geneID Count
## GO:0000307      RB1/CCND1/CDKN1A     3
## GO:1902554      RB1/CCND1/CDKN1A     3
## GO:0016514            RB1/ARID1A     2
## GO:1902911      RB1/CCND1/CDKN1A     3
## GO:0005925 KRAS/PTK2/YWHAZ/ITGA2     4
## GO:0030055 KRAS/PTK2/YWHAZ/ITGA2     4
##                    ID                             Description GeneRatio
## GO:0008190 GO:0008190 eukaryotic initiation factor 4E binding      2/35
## GO:0003684 GO:0003684                     damaged DNA binding      3/35
## GO:0019887 GO:0019887       protein kinase regulator activity      4/35
## GO:0001221 GO:0001221       transcription coregulator binding      3/35
## GO:0019207 GO:0019207               kinase regulator activity      4/35
## GO:0031369 GO:0031369   translation initiation factor binding      2/35
##              BgRatio       pvalue   p.adjust     qvalue                  geneID
## GO:0008190  10/18522 0.0001546248 0.03741919 0.02164747         EIF4EBP1/EIF4G1
## GO:0003684  73/18522 0.0003511289 0.04248659 0.02457902        XRCC5/TP63/PARP1
## GO:0019887 232/18522 0.0009258617 0.04890590 0.02829267 ERBB3/CCNB1/YWHAB/CCNE2
## GO:0001221 114/18522 0.0012875289 0.04890590 0.02829267           GATA3/AR/EZH2
## GO:0019207 270/18522 0.0016203361 0.04890590 0.02829267 ERBB3/CCNB1/YWHAB/CCNE2
## GO:0031369  32/18522 0.0016604070 0.04890590 0.02829267         EIF4EBP1/EIF4G1
##            Count
## GO:0008190     2
## GO:0003684     3
## GO:0019887     4
## GO:0001221     3
## GO:0019207     4
## GO:0031369     2
##                    ID                                        Description
## GO:0045931 GO:0045931          positive regulation of mitotic cell cycle
## GO:0032200 GO:0032200                              telomere organization
## GO:0045859 GO:0045859              regulation of protein kinase activity
## GO:0045787 GO:0045787                  positive regulation of cell cycle
## GO:1901989 GO:1901989 positive regulation of cell cycle phase transition
## GO:1902298 GO:1902298 cell cycle DNA replication maintenance of fidelity
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0045931      6/36 130/18888 1.556436e-07 0.0003052171 0.0001720272
## GO:0032200      6/36 189/18888 1.406881e-06 0.0007847751 0.0004423167
## GO:0045859      8/36 470/18888 2.271196e-06 0.0007847751 0.0004423167
## GO:0045787      7/36 332/18888 2.621030e-06 0.0007847751 0.0004423167
## GO:1901989      5/36 117/18888 2.706115e-06 0.0007847751 0.0004423167
## GO:1902298      2/36   2/18888 3.532007e-06 0.0007847751 0.0004423167
##                                                   geneID Count
## GO:0045931        EIF4EBP1/EIF4G1/BRCA2/CDK1/CCNB1/CCNE2     6
## GO:0032200            RAD51/XRCC5/BRCA2/EZH2/CCNE2/PARP1     6
## GO:0045859 XRCC5/ADAR/PDCD4/PTK2/CCNB1/EZH2/CCNE2/ERRFI1     8
## GO:0045787   EIF4EBP1/EIF4G1/BRCA2/CDK1/CCNB1/EZH2/CCNE2     7
## GO:1901989                  EIF4G1/CDK1/CCNB1/EZH2/CCNE2     5
## GO:1902298                                   RAD51/BRCA2     2
##                    ID                                        Description
## GO:0000781 GO:0000781                       chromosome, telomeric region
## GO:0097125 GO:0097125                             cyclin B1-CDK1 complex
## GO:0098687 GO:0098687                                 chromosomal region
## GO:1902554 GO:1902554            serine/threonine protein kinase complex
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:1902911 GO:1902911                             protein kinase complex
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0000781      6/36 173/19894 6.219983e-07 0.0001156917 6.940191e-05
## GO:0097125      2/36   2/19894 3.183817e-06 0.0002960950 1.776235e-04
## GO:0098687      7/36 402/19894 6.571942e-06 0.0004074604 2.444301e-04
## GO:1902554      4/36 136/19894 1.038614e-04 0.0046992349 2.819009e-03
## GO:0000307      3/36  56/19894 1.412264e-04 0.0046992349 2.819009e-03
## GO:1902911      4/36 150/19894 1.515882e-04 0.0046992349 2.819009e-03
##                                             geneID Count
## GO:0000781       RAD51/XRCC5/BRCA2/CDK1/EZH2/PARP1     6
## GO:0097125                              CDK1/CCNB1     2
## GO:0098687 RAD51/XRCC5/BRCA2/CDK1/CCNB1/EZH2/PARP1     7
## GO:1902554                  XRCC5/CDK1/CCNB1/CCNE2     4
## GO:0000307                        CDK1/CCNB1/CCNE2     3
## GO:1902911                  XRCC5/CDK1/CCNB1/CCNE2     4
##                    ID                               Description GeneRatio
## GO:0032143 GO:0032143          single thymine insertion binding      2/30
## GO:0035173 GO:0035173                   histone kinase activity      3/30
## GO:0032137 GO:0032137           guanine/thymine mispair binding      2/30
## GO:0032142 GO:0032142          single guanine insertion binding      2/30
## GO:0032138 GO:0032138 single base insertion or deletion binding      2/30
## GO:0032135 GO:0032135         DNA insertion or deletion binding      2/30
##             BgRatio       pvalue     p.adjust       qvalue         geneID Count
## GO:0032143  2/18522 2.536103e-06 0.0004180353 0.0002000169      MSH6/MSH2     2
## GO:0035173 23/18522 6.643582e-06 0.0004180353 0.0002000169 PRKCA/CDK1/ATM     3
## GO:0032137  3/18522 7.600641e-06 0.0004180353 0.0002000169      MSH6/MSH2     2
## GO:0032142  3/18522 7.600641e-06 0.0004180353 0.0002000169      MSH6/MSH2     2
## GO:0032138  4/18522 1.518596e-05 0.0006681823 0.0003197045      MSH6/MSH2     2
## GO:0032135  6/18522 3.788843e-05 0.0011907792 0.0005697508      MSH6/MSH2     2
##                    ID
## GO:0010165 GO:0010165
## GO:0002520 GO:0002520
## GO:0045785 GO:0045785
## GO:0002285 GO:0002285
## GO:0051053 GO:0051053
## GO:0002562 GO:0002562
##                                                                                             Description
## GO:0010165                                                                            response to X-ray
## GO:0002520                                                                    immune system development
## GO:0045785                                                         positive regulation of cell adhesion
## GO:0002285                                            lymphocyte activation involved in immune response
## GO:0051053                                                 negative regulation of DNA metabolic process
## GO:0002562 somatic diversification of immune receptors via germline recombination within a single locus
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0010165      4/30  28/18888 1.030795e-07 0.0001804922 9.613521e-05
## GO:0002520      6/30 197/18888 5.749726e-07 0.0003706617 1.974248e-04
## GO:0045785      8/30 485/18888 6.350572e-07 0.0003706617 1.974248e-04
## GO:0002285      6/30 212/18888 8.833118e-07 0.0003866698 2.059511e-04
## GO:0051053      5/30 142/18888 2.741088e-06 0.0009599292 5.112851e-04
## GO:0002562      4/30  70/18888 4.407252e-06 0.0011024427 5.871918e-04
##                                                 geneID Count
## GO:0010165                        GATA3/ATM/BRCA2/MSH2     4
## GO:0002520              RBM15/GATA3/ATM/MSH6/TFRC/MSH2     6
## GO:0045785 PRKCA/IGFBP2/GATA3/ATM/TSC1/XBP1/TFRC/PREX1     8
## GO:0002285              GATA3/TSC1/XBP1/MSH6/TFRC/MSH2     6
## GO:0051053                    GATA3/ATM/TTF1/MSH6/MSH2     5
## GO:0002562                          ATM/MSH6/TFRC/MSH2     4
##                    ID                  Description GeneRatio   BgRatio
## GO:0042470 GO:0042470                   melanosome      5/30 112/19894
## GO:0048770 GO:0048770              pigment granule      5/30 112/19894
## GO:0032301 GO:0032301            MutSalpha complex      2/30   2/19894
## GO:0097125 GO:0097125       cyclin B1-CDK1 complex      2/30   2/19894
## GO:0032300 GO:0032300      mismatch repair complex      2/30  11/19894
## GO:0000781 GO:0000781 chromosome, telomeric region      4/30 173/19894
##                  pvalue     p.adjust       qvalue                      geneID
## GO:0042470 6.584008e-07 4.016245e-05 2.772214e-05 FASN/YWHAB/PRDX1/MYH11/TFRC
## GO:0048770 6.584008e-07 4.016245e-05 2.772214e-05 FASN/YWHAB/PRDX1/MYH11/TFRC
## GO:0032301 2.198350e-06 6.704968e-05 4.628105e-05                   MSH6/MSH2
## GO:0097125 2.198350e-06 6.704968e-05 4.628105e-05                  CDK1/CCNB1
## GO:0032300 1.198923e-04 2.579428e-03 1.780451e-03                   MSH6/MSH2
## GO:0000781 1.268571e-04 2.579428e-03 1.780451e-03         CDK1/ATM/BRCA2/MSH2
##            Count
## GO:0042470     5
## GO:0048770     5
## GO:0032301     2
## GO:0097125     2
## GO:0032300     2
## GO:0000781     4
##                    ID                              Description GeneRatio
## GO:0120283 GO:0120283  protein serine/threonine kinase binding      2/23
## GO:0106310 GO:0106310           protein serine kinase activity      5/23
## GO:0004674 GO:0004674 protein serine/threonine kinase activity      5/23
## GO:0004707 GO:0004707                      MAP kinase activity      2/23
## GO:0070064 GO:0070064              proline-rich region binding      2/23
## GO:0042826 GO:0042826              histone deacetylase binding      3/23
##              BgRatio       pvalue    p.adjust      qvalue
## GO:0120283   7/18522 3.085855e-05 0.005523681 0.002273788
## GO:0106310 363/18522 7.075911e-05 0.006332941 0.002606915
## GO:0004674 427/18522 1.518718e-04 0.007100610 0.002922921
## GO:0004707  16/18522 1.751391e-04 0.007100610 0.002922921
## GO:0070064  17/18522 1.983411e-04 0.007100610 0.002922921
## GO:0042826 128/18522 5.160029e-04 0.015394085 0.006336877
##                               geneID Count
## GO:0120283                MAPK8/XIAP     2
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004707               MAPK8/MAPK1     2
## GO:0070064                CCND1/YAP1     2
## GO:0042826        HSPA1A/MAPK8/CCND1     3
##                    ID                                 Description GeneRatio
## GO:0010631 GO:0010631                   epithelial cell migration      9/23
## GO:0090132 GO:0090132                        epithelium migration      9/23
## GO:0090130 GO:0090130                            tissue migration      9/23
## GO:0001667 GO:0001667               ameboidal-type cell migration      9/23
## GO:0071214 GO:0071214       cellular response to abiotic stimulus      8/23
## GO:0104004 GO:0104004 cellular response to environmental stimulus      8/23
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0010631 375/18888 2.784961e-10 2.143530e-07 8.314100e-08
## GO:0090132 378/18888 2.988249e-10 2.143530e-07 8.314100e-08
## GO:0090130 383/18888 3.356258e-10 2.143530e-07 8.314100e-08
## GO:0001667 498/18888 3.370825e-09 1.092718e-06 4.238319e-07
## GO:0071214 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## GO:0104004 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
##                                                     geneID Count
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0001667 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0071214     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
## GO:0104004     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
##                    ID                  Description GeneRatio   BgRatio
## GO:0005925 GO:0005925               focal adhesion      6/23 421/19894
## GO:0030055 GO:0030055      cell-substrate junction      6/23 431/19894
## GO:0005826 GO:0005826  actomyosin contractile ring      2/23   4/19894
## GO:0070938 GO:0070938             contractile ring      2/23  10/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane      4/23 219/19894
## GO:0031968 GO:0031968     organelle outer membrane      4/23 248/19894
##                  pvalue     p.adjust       qvalue
## GO:0005925 6.447048e-06 0.0003166418 0.0001720295
## GO:0030055 7.373490e-06 0.0003166418 0.0001720295
## GO:0005826 7.660689e-06 0.0003166418 0.0001720295
## GO:0070938 5.721303e-05 0.0017736039 0.0009635879
## GO:0005741 1.073470e-04 0.0026622052 0.0014463593
## GO:0031968 1.732117e-04 0.0031642699 0.0017191279
##                                       geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1     6
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1     6
## GO:0005826                         MYH9/ANLN     2
## GO:0070938                         MYH9/ANLN     2
## GO:0005741             MTOR/FOXO3/CASP8/KRAS     4
## GO:0031968             MTOR/FOXO3/CASP8/KRAS     4
##                    ID
## GO:0120283 GO:0120283
## GO:0140297 GO:0140297
## GO:0031625 GO:0031625
## GO:0044389 GO:0044389
## GO:0061629 GO:0061629
## GO:0140311 GO:0140311
##                                                                    Description
## GO:0120283                             protein serine/threonine kinase binding
## GO:0140297                            DNA-binding transcription factor binding
## GO:0031625                                    ubiquitin protein ligase binding
## GO:0044389                               ubiquitin-like protein ligase binding
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GO:0140311                                       protein sequestering activity
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0120283      2/17   7/18522 1.660593e-05 0.002358042 0.0008914761
## GO:0140297      5/17 478/18522 5.365384e-05 0.003809423 0.0014401820
## GO:0031625      4/17 305/18522 1.448503e-04 0.006454095 0.0024400209
## GO:0044389      4/17 324/18522 1.827003e-04 0.006454095 0.0024400209
## GO:0061629      4/17 343/18522 2.272569e-04 0.006454095 0.0024400209
## GO:0140311      2/17  29/18522 3.172573e-04 0.007508423 0.0028386181
##                                 geneID Count
## GO:0120283                  XIAP/MAPK8     2
## GO:0140297 RB1/ETS1/ARID1A/YWHAZ/NCOA3     5
## GO:0031625        RB1/BID/YWHAZ/CDKN1A     4
## GO:0044389        RB1/BID/YWHAZ/CDKN1A     4
## GO:0061629       RB1/ETS1/ARID1A/NCOA3     4
## GO:0140311                YWHAZ/CDKN1A     2
##                    ID
## GO:2000045 GO:2000045
## GO:1902806 GO:1902806
## GO:0000082 GO:0000082
## GO:0044843 GO:0044843
## GO:2000134 GO:2000134
## GO:1901990 GO:1901990
##                                                             Description
## GO:2000045          regulation of G1/S transition of mitotic cell cycle
## GO:1902806               regulation of cell cycle G1/S phase transition
## GO:0000082                        G1/S transition of mitotic cell cycle
## GO:0044843                             cell cycle G1/S phase transition
## GO:2000134 negative regulation of G1/S transition of mitotic cell cycle
## GO:1901990            regulation of mitotic cell cycle phase transition
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:2000045      7/17 185/18888 1.381696e-10 1.692577e-07 7.359348e-08
## GO:1902806      7/17 211/18888 3.476363e-10 2.129273e-07 9.258105e-08
## GO:0000082      7/17 234/18888 7.166752e-10 2.926424e-07 1.272413e-07
## GO:0044843      7/17 262/18888 1.575684e-09 4.825534e-07 2.098148e-07
## GO:2000134      5/17  85/18888 9.716264e-09 2.380485e-06 1.035038e-06
## GO:1901990      7/17 356/18888 1.317298e-08 2.689483e-06 1.169391e-06
##                                          geneID Count
## GO:2000045 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A     7
## GO:1902806 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A     7
## GO:0000082 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A     7
## GO:0044843 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A     7
## GO:2000134            RB1/PTEN/ATM/CCND1/CDKN1A     5
## GO:1901990 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A     7
##                    ID                                        Description
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:1902554 GO:1902554            serine/threonine protein kinase complex
## GO:1902911 GO:1902911                             protein kinase complex
## GO:0016514 GO:0016514                                    SWI/SNF complex
## GO:0005925 GO:0005925                                     focal adhesion
## GO:0030055 GO:0030055                            cell-substrate junction
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0000307      3/17  56/19894 1.397003e-05 0.001117602 0.0005735065
## GO:1902554      3/17 136/19894 1.980967e-04 0.005510756 0.0028278880
## GO:1902911      3/17 150/19894 2.643788e-04 0.005510756 0.0028278880
## GO:0016514      2/17  30/19894 2.947971e-04 0.005510756 0.0028278880
## GO:0005925      4/17 421/19894 3.781266e-04 0.005510756 0.0028278880
## GO:0030055      4/17 431/19894 4.133067e-04 0.005510756 0.0028278880
##                           geneID Count
## GO:0000307      RB1/CCND1/CDKN1A     3
## GO:1902554      RB1/CCND1/CDKN1A     3
## GO:1902911      RB1/CCND1/CDKN1A     3
## GO:0016514            RB1/ARID1A     2
## GO:0005925 KRAS/PTK2/YWHAZ/ITGA2     4
## GO:0030055 KRAS/PTK2/YWHAZ/ITGA2     4
##                    ID                              Description GeneRatio
## GO:0045296 GO:0045296                         cadherin binding     12/62
## GO:0140297 GO:0140297 DNA-binding transcription factor binding     12/62
## GO:0019903 GO:0019903              protein phosphatase binding      7/62
## GO:0031625 GO:0031625         ubiquitin protein ligase binding      9/62
## GO:0044389 GO:0044389    ubiquitin-like protein ligase binding      9/62
## GO:0019902 GO:0019902                      phosphatase binding      7/62
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0045296 333/18522 9.037285e-10 3.533578e-07 1.702815e-07
## GO:0140297 478/18522 5.094827e-08 9.960387e-06 4.799863e-06
## GO:0019903 142/18522 4.640913e-07 6.048657e-05 2.914819e-05
## GO:0031625 305/18522 7.466285e-07 7.298293e-05 3.517013e-05
## GO:0044389 324/18522 1.232957e-06 9.641722e-05 4.646300e-05
## GO:0019902 189/18522 3.155486e-06 2.056325e-04 9.909334e-05
##                                                                         geneID
## GO:0045296 EGFR/CDH1/MYH9/YWHAZ/NDRG1/CTNNA1/PRDX1/YWHAB/NOTCH3/EEF2/VASP/FASN
## GO:0140297      SMAD4/RB1/E2F1/MYC/YWHAZ/NCOA3/PARP1/JUN/TP53/STAT3/ARID1A/VHL
## GO:0019903                                EGFR/MET/MAPK8/CDKN1B/PXN/TP53/STAT3
## GO:0031625                   EGFR/TUBA1B/RB1/YWHAZ/CASP8/PARP1/CDKN1B/JUN/TP53
## GO:0044389                   EGFR/TUBA1B/RB1/YWHAZ/CASP8/PARP1/CDKN1B/JUN/TP53
## GO:0019902                                EGFR/MET/MAPK8/CDKN1B/PXN/TP53/STAT3
##            Count
## GO:0045296    12
## GO:0140297    12
## GO:0019903     7
## GO:0031625     9
## GO:0044389     9
## GO:0019902     7
##                    ID                           Description GeneRatio   BgRatio
## GO:0062197 GO:0062197  cellular response to chemical stress     15/62 311/18888
## GO:0051402 GO:0051402              neuron apoptotic process     14/62 292/18888
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle     13/62 234/18888
## GO:0034599 GO:0034599 cellular response to oxidative stress     13/62 248/18888
## GO:0097305 GO:0097305                   response to alcohol     13/62 259/18888
## GO:0044843 GO:0044843      cell cycle G1/S phase transition     13/62 262/18888
##                  pvalue     p.adjust       qvalue
## GO:0062197 5.868369e-14 1.839734e-10 7.993337e-11
## GO:0051402 4.880667e-13 5.885847e-10 2.557303e-10
## GO:0000082 5.632390e-13 5.885847e-10 2.557303e-10
## GO:0034599 1.181483e-12 9.259874e-10 4.023261e-10
## GO:0097305 2.050313e-12 1.181391e-09 5.132948e-10
## GO:0044843 2.372544e-12 1.181391e-09 5.132948e-10
##                                                                                    geneID
## GO:0062197   EGFR/MET/AKT1/CASP3/ATM/MAPK8/PARP1/MTOR/PRDX1/PRKAA1/PXN/JUN/TP53/G6PD/CDK1
## GO:0051402 BCL2L1/CASP3/ATM/XIAP/RB1/CASP8/PARP1/BCL2L11/TP53/AKT2/GAPDH/AKT1S1/G6PD/MSH2
## GO:0000082        EGFR/AKT1/ATM/RB1/E2F1/MYC/EIF4EBP1/CDKN1B/TP53/EIF4G1/ARID1A/PTEN/CDK1
## GO:0034599              EGFR/MET/AKT1/ATM/MAPK8/PARP1/PRDX1/PRKAA1/PXN/JUN/TP53/G6PD/CDK1
## GO:0097305  AKT1/BCL2L1/IGF1R/CDH1/CASP8/RAD51/PARP1/CTNNA1/PRKAA1/EIF4G1/PTCH1/G6PD/CDK1
## GO:0044843        EGFR/AKT1/ATM/RB1/E2F1/MYC/EIF4EBP1/CDKN1B/TP53/EIF4G1/ARID1A/PTEN/CDK1
##            Count
## GO:0062197    15
## GO:0051402    14
## GO:0000082    13
## GO:0034599    13
## GO:0097305    13
## GO:0044843    13
##                    ID                                       Description
## GO:0031252 GO:0031252                                 cell leading edge
## GO:0030027 GO:0030027                                     lamellipodium
## GO:0005901 GO:0005901                                           caveola
## GO:0038201 GO:0038201                                       TOR complex
## GO:0090575 GO:0090575 RNA polymerase II transcription regulator complex
## GO:0016605 GO:0016605                                          PML body
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0031252     11/62 426/19894 7.269174e-08 1.744602e-05 8.799526e-06
## GO:0030027      7/62 203/19894 3.176241e-06 3.729449e-04 1.881082e-04
## GO:0005901      5/62  82/19894 5.659915e-06 3.729449e-04 1.881082e-04
## GO:0038201      3/62  12/19894 6.215748e-06 3.729449e-04 1.881082e-04
## GO:0090575      7/62 255/19894 1.411896e-05 6.777100e-04 3.418274e-04
## GO:0016605      5/62 108/19894 2.173211e-05 7.211011e-04 3.637133e-04
##                                                              geneID Count
## GO:0031252 EGFR/AKT1/CDH1/NF2/MYH9/CASP8/CTNNA1/PXN/ERBB2/AKT2/VASP    11
## GO:0030027                      AKT1/CDH1/NF2/CASP8/CTNNA1/PXN/VASP     7
## GO:0005901                             IGF1R/CDH1/CTNNA1/PTCH1/IRS1     5
## GO:0038201                                       MTOR/AKT1S1/RICTOR     3
## GO:0090575                        SMAD4/RB1/E2F1/MYC/JUN/XBP1/STAT3     7
## GO:0016605                                 RB1/RAD51/MTOR/TP53/PTEN     5
##                    ID                               Description GeneRatio
## GO:0003684 GO:0003684                       damaged DNA binding      4/35
## GO:0043125 GO:0043125             ErbB-3 class receptor binding      2/35
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding      3/35
## GO:0004707 GO:0004707                       MAP kinase activity      2/35
## GO:0019902 GO:0019902                       phosphatase binding      4/35
## GO:0051219 GO:0051219                    phosphoprotein binding      3/35
##              BgRatio       pvalue    p.adjust      qvalue
## GO:0003684  73/18522 1.059881e-05 0.002458925 0.001383424
## GO:0043125   5/18522 3.456577e-05 0.004009629 0.002255871
## GO:0045309  59/18522 1.868833e-04 0.014452308 0.008131062
## GO:0004707  16/18522 4.094059e-04 0.019921948 0.011208355
## GO:0019902 189/18522 4.293523e-04 0.019921948 0.011208355
## GO:0051219  93/18522 7.139065e-04 0.027604384 0.015530597
##                            geneID Count
## GO:0003684 XRCC5/TP63/ERCC1/PARP1     4
## GO:0043125             ERBB3/NRG1     2
## GO:0045309        MAPK1/LCK/YWHAB     3
## GO:0004707           MAPK14/MAPK1     2
## GO:0019902  MAPK14/MAPK1/PTK2/LCK     4
## GO:0051219        MAPK1/LCK/YWHAB     3
##                    ID                                 Description GeneRatio
## GO:0071478 GO:0071478              cellular response to radiation      8/36
## GO:0010212 GO:0010212              response to ionizing radiation      7/36
## GO:0061180 GO:0061180        mammary gland epithelium development      5/36
## GO:0071214 GO:0071214       cellular response to abiotic stimulus      8/36
## GO:0104004 GO:0104004 cellular response to environmental stimulus      8/36
## GO:0030879 GO:0030879                   mammary gland development      6/36
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0071478 181/18888 1.465387e-09 3.001113e-06 1.613468e-06
## GO:0010212 138/18888 6.669773e-09 6.829848e-06 3.671886e-06
## GO:0061180  67/18888 1.670382e-07 5.637465e-05 3.030833e-05
## GO:0071214 334/18888 1.728301e-07 5.637465e-05 3.030833e-05
## GO:0104004 334/18888 1.728301e-07 5.637465e-05 3.030833e-05
## GO:0030879 135/18888 1.947229e-07 5.637465e-05 3.030833e-05
##                                                     geneID Count
## GO:0071478 MAPK14/AKT2/RAD51/GATA3/XRCC5/BRCA2/ERCC1/PARP1     8
## GO:0010212      MAPK14/RAD51/GATA3/XRCC5/BRCA2/ERCC1/PARP1     7
## GO:0061180                       AKT2/GATA3/MAPK1/BRCA2/AR     5
## GO:0071214 MAPK14/AKT2/RAD51/GATA3/XRCC5/BRCA2/ERCC1/PARP1     8
## GO:0104004 MAPK14/AKT2/RAD51/GATA3/XRCC5/BRCA2/ERCC1/PARP1     8
## GO:0030879                  AKT2/GATA3/MAPK1/BRCA2/AR/NRG1     6
##                    ID                  Description GeneRatio   BgRatio
## GO:0000781 GO:0000781 chromosome, telomeric region      5/36 173/19894
## GO:0000800 GO:0000800              lateral element      2/36  14/19894
## GO:0031143 GO:0031143                 pseudopodium      2/36  18/19894
## GO:1990391 GO:1990391           DNA repair complex      2/36  22/19894
## GO:0098687 GO:0098687           chromosomal region      5/36 402/19894
## GO:0090734 GO:0090734           site of DNA damage      3/36 123/19894
##                  pvalue    p.adjust      qvalue                        geneID
## GO:0000781 1.422251e-05 0.002474716 0.001527048 RAD51/XRCC5/BRCA2/ERCC1/PARP1
## GO:0000800 2.857927e-04 0.024863964 0.015342555                   RAD51/BRCA2
## GO:0031143 4.783253e-04 0.025735885 0.015880583                   MAPK1/RAB25
## GO:1990391 7.188974e-04 0.025735885 0.015880583                   XRCC5/BRCA2
## GO:0098687 7.395369e-04 0.025735885 0.015880583 RAD51/XRCC5/BRCA2/ERCC1/PARP1
## GO:0090734 1.418836e-03 0.041146250 0.025389701             RAD51/XRCC5/PARP1
##            Count
## GO:0000781     5
## GO:0000800     2
## GO:0031143     2
## GO:1990391     2
## GO:0098687     5
## GO:0090734     3
##                    ID                               Description GeneRatio
## GO:0032143 GO:0032143          single thymine insertion binding      2/27
## GO:0035173 GO:0035173                   histone kinase activity      3/27
## GO:0032137 GO:0032137           guanine/thymine mispair binding      2/27
## GO:0032142 GO:0032142          single guanine insertion binding      2/27
## GO:0032138 GO:0032138 single base insertion or deletion binding      2/27
## GO:0032135 GO:0032135         DNA insertion or deletion binding      2/27
##             BgRatio       pvalue     p.adjust       qvalue         geneID Count
## GO:0032143  2/18522 2.046373e-06 0.0003005461 0.0001371988      MSH6/MSH2     2
## GO:0035173 23/18522 4.797970e-06 0.0003005461 0.0001371988 PRKCA/CDK1/ATM     3
## GO:0032137  3/18522 6.133594e-06 0.0003005461 0.0001371988      MSH6/MSH2     2
## GO:0032142  3/18522 6.133594e-06 0.0003005461 0.0001371988      MSH6/MSH2     2
## GO:0032138  4/18522 1.225615e-05 0.0004804411 0.0002193206      MSH6/MSH2     2
## GO:0032135  6/18522 3.058526e-05 0.0008563873 0.0003909394      MSH6/MSH2     2
##                    ID                                       Description
## GO:0010165 GO:0010165                                 response to X-ray
## GO:0045785 GO:0045785              positive regulation of cell adhesion
## GO:0002520 GO:0002520                         immune system development
## GO:0002285 GO:0002285 lymphocyte activation involved in immune response
## GO:0045931 GO:0045931         positive regulation of mitotic cell cycle
## GO:0051053 GO:0051053      negative regulation of DNA metabolic process
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0010165      4/27  28/18888 6.621328e-08 0.0001052791 5.429489e-05
## GO:0045785      8/27 485/18888 2.577809e-07 0.0001559259 8.041462e-05
## GO:0002520      6/27 197/18888 2.941998e-07 0.0001559259 8.041462e-05
## GO:0002285      6/27 212/18888 4.528952e-07 0.0001800258 9.284351e-05
## GO:0045931      5/27 130/18888 1.022030e-06 0.0003250055 1.676129e-04
## GO:0051053      5/27 142/18888 1.581256e-06 0.0004190327 2.161049e-04
##                                                 geneID Count
## GO:0010165                        GATA3/ATM/BRCA2/MSH2     4
## GO:0045785 PRKCA/PREX1/IGFBP2/GATA3/ATM/TSC1/XBP1/TFRC     8
## GO:0002520              MSH6/RBM15/GATA3/ATM/TFRC/MSH2     6
## GO:0002285              MSH6/GATA3/TSC1/XBP1/TFRC/MSH2     6
## GO:0045931                 PRKCA/CDK1/CCNB1/ASNS/BRCA2     5
## GO:0051053                    MSH6/GATA3/ATM/TTF1/MSH2     5
##                    ID                  Description GeneRatio   BgRatio
## GO:0032301 GO:0032301            MutSalpha complex      2/27   2/19894
## GO:0097125 GO:0097125       cyclin B1-CDK1 complex      2/27   2/19894
## GO:0042470 GO:0042470                   melanosome      4/27 112/19894
## GO:0048770 GO:0048770              pigment granule      4/27 112/19894
## GO:0000781 GO:0000781 chromosome, telomeric region      4/27 173/19894
## GO:0032300 GO:0032300      mismatch repair complex      2/27  11/19894
##                  pvalue     p.adjust       qvalue                geneID Count
## GO:0032301 1.773841e-06 0.0001011089 7.655525e-05             MSH6/MSH2     2
## GO:0097125 1.773841e-06 0.0001011089 7.655525e-05            CDK1/CCNB1     2
## GO:0042470 1.511691e-05 0.0004308319 3.262069e-04 FASN/PRDX1/MYH11/TFRC     4
## GO:0048770 1.511691e-05 0.0004308319 3.262069e-04 FASN/PRDX1/MYH11/TFRC     4
## GO:0000781 8.290780e-05 0.0018397365 1.392968e-03   CDK1/ATM/BRCA2/MSH2     4
## GO:0032300 9.682824e-05 0.0018397365 1.392968e-03             MSH6/MSH2     2
##                    ID                              Description GeneRatio
## GO:0120283 GO:0120283  protein serine/threonine kinase binding      2/23
## GO:0106310 GO:0106310           protein serine kinase activity      5/23
## GO:0004674 GO:0004674 protein serine/threonine kinase activity      5/23
## GO:0004707 GO:0004707                      MAP kinase activity      2/23
## GO:0070064 GO:0070064              proline-rich region binding      2/23
## GO:0042826 GO:0042826              histone deacetylase binding      3/23
##              BgRatio       pvalue    p.adjust      qvalue
## GO:0120283   7/18522 3.085855e-05 0.005523681 0.002273788
## GO:0106310 363/18522 7.075911e-05 0.006332941 0.002606915
## GO:0004674 427/18522 1.518718e-04 0.007100610 0.002922921
## GO:0004707  16/18522 1.751391e-04 0.007100610 0.002922921
## GO:0070064  17/18522 1.983411e-04 0.007100610 0.002922921
## GO:0042826 128/18522 5.160029e-04 0.015394085 0.006336877
##                               geneID Count
## GO:0120283                MAPK8/XIAP     2
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004707               MAPK8/MAPK1     2
## GO:0070064                CCND1/YAP1     2
## GO:0042826        HSPA1A/MAPK8/CCND1     3
##                    ID                                 Description GeneRatio
## GO:0010631 GO:0010631                   epithelial cell migration      9/23
## GO:0090132 GO:0090132                        epithelium migration      9/23
## GO:0090130 GO:0090130                            tissue migration      9/23
## GO:0001667 GO:0001667               ameboidal-type cell migration      9/23
## GO:0071214 GO:0071214       cellular response to abiotic stimulus      8/23
## GO:0104004 GO:0104004 cellular response to environmental stimulus      8/23
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0010631 375/18888 2.784961e-10 2.143530e-07 8.314100e-08
## GO:0090132 378/18888 2.988249e-10 2.143530e-07 8.314100e-08
## GO:0090130 383/18888 3.356258e-10 2.143530e-07 8.314100e-08
## GO:0001667 498/18888 3.370825e-09 1.092718e-06 4.238319e-07
## GO:0071214 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## GO:0104004 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
##                                                     geneID Count
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0001667 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN     9
## GO:0071214     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
## GO:0104004     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
##                    ID                  Description GeneRatio   BgRatio
## GO:0005925 GO:0005925               focal adhesion      6/23 421/19894
## GO:0030055 GO:0030055      cell-substrate junction      6/23 431/19894
## GO:0005826 GO:0005826  actomyosin contractile ring      2/23   4/19894
## GO:0070938 GO:0070938             contractile ring      2/23  10/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane      4/23 219/19894
## GO:0031968 GO:0031968     organelle outer membrane      4/23 248/19894
##                  pvalue     p.adjust       qvalue
## GO:0005925 6.447048e-06 0.0003166418 0.0001720295
## GO:0030055 7.373490e-06 0.0003166418 0.0001720295
## GO:0005826 7.660689e-06 0.0003166418 0.0001720295
## GO:0070938 5.721303e-05 0.0017736039 0.0009635879
## GO:0005741 1.073470e-04 0.0026622052 0.0014463593
## GO:0031968 1.732117e-04 0.0031642699 0.0017191279
##                                       geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1     6
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1     6
## GO:0005826                         MYH9/ANLN     2
## GO:0070938                         MYH9/ANLN     2
## GO:0005741             MTOR/FOXO3/CASP8/KRAS     4
## GO:0031968             MTOR/FOXO3/CASP8/KRAS     4
##                    ID
## GO:0003684 GO:0003684
## GO:0032139 GO:0032139
## GO:1990599 GO:1990599
## GO:0106017 GO:0106017
## GO:0032135 GO:0032135
## GO:0032405 GO:0032405
##                                                               Description
## GO:0003684                                            damaged DNA binding
## GO:0032139                     dinucleotide insertion or deletion binding
## GO:1990599 3' overhang single-stranded DNA endodeoxyribonuclease activity
## GO:0106017     phosphatidylinositol-3,4-bisphosphate phosphatase activity
## GO:0032135                              DNA insertion or deletion binding
## GO:0032405                                      MutLalpha complex binding
##            GeneRatio  BgRatio       pvalue     p.adjust       qvalue
## GO:0003684      4/27 73/18522 3.638183e-06 0.0004763758 0.0001915403
## GO:0032139      2/27  3/18522 6.133594e-06 0.0004763758 0.0001915403
## GO:1990599      2/27  3/18522 6.133594e-06 0.0004763758 0.0001915403
## GO:0106017      2/27  4/18522 1.225615e-05 0.0007139207 0.0002870519
## GO:0032135      2/27  6/18522 3.058526e-05 0.0011877276 0.0004775593
## GO:0032405      2/27  6/18522 3.058526e-05 0.0011877276 0.0004775593
##                           geneID Count
## GO:0003684 PCNA/XRCC1/ERCC1/MSH2     4
## GO:0032139             PCNA/MSH2     2
## GO:1990599           XRCC1/ERCC1     2
## GO:0106017           PTEN/INPP4B     2
## GO:0032135             PCNA/MSH2     2
## GO:0032405             PCNA/MSH2     2
##                    ID                                  Description GeneRatio
## GO:0010165 GO:0010165                            response to X-ray      5/27
## GO:0051054 GO:0051054 positive regulation of DNA metabolic process      8/27
## GO:0006312 GO:0006312                        mitotic recombination      4/27
## GO:0006979 GO:0006979                 response to oxidative stress      8/27
## GO:0048732 GO:0048732                            gland development      8/27
## GO:1904354 GO:1904354      negative regulation of telomere capping      3/27
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0010165  28/18888 3.875046e-10 7.606715e-07 3.491620e-07
## GO:0051054 301/18888 6.468898e-09 6.349223e-06 2.914409e-06
## GO:0006312  25/18888 4.102815e-08 2.684608e-05 1.232284e-05
## GO:0006979 398/18888 5.664809e-08 2.780005e-05 1.276073e-05
## GO:0048732 449/18888 1.430479e-07 4.749793e-05 2.180241e-05
## GO:1904354   8/18888 1.451796e-07 4.749793e-05 2.180241e-05
##                                               geneID Count
## GO:0010165                GATA3/ATM/BRCA2/ERCC1/MSH2     5
## GO:0051054  ATM/EGFR/PCNA/CDK1/XRCC1/ERCC1/TFRC/MSH2     8
## GO:0006312                    BRCA2/XRCC1/ERCC1/MSH2     4
## GO:0006979 G6PD/ATM/EGFR/PCNA/CDK1/XRCC1/PRDX1/ERCC1     8
## GO:0048732    GATA3/ATM/BRCA2/EGFR/FASN/PCNA/AR/XBP1     8
## GO:1904354                           ATM/XRCC1/ERCC1     3
##                    ID                        Description GeneRatio   BgRatio
## GO:0000781 GO:0000781       chromosome, telomeric region      7/27 173/19894
## GO:0098687 GO:0098687                 chromosomal region      7/27 402/19894
## GO:0070522 GO:0070522                ERCC4-ERCC1 complex      2/27   4/19894
## GO:0000109 GO:0000109 nucleotide-excision repair complex      2/27  12/19894
## GO:1990391 GO:1990391                 DNA repair complex      2/27  22/19894
## GO:0042470 GO:0042470                         melanosome      3/27 112/19894
##                  pvalue     p.adjust       qvalue
## GO:0000781 2.553497e-09 3.319546e-07 2.042797e-07
## GO:0098687 8.178489e-07 5.316018e-05 3.271396e-05
## GO:0070522 1.062522e-05 4.604262e-04 2.833392e-04
## GO:0000109 1.160966e-04 3.773139e-03 2.321932e-03
## GO:1990391 4.029496e-04 8.550575e-03 5.261892e-03
## GO:0042470 4.604156e-04 8.550575e-03 5.261892e-03
##                                          geneID Count
## GO:0000781 ATM/BRCA2/PCNA/CDK1/XRCC1/ERCC1/MSH2     7
## GO:0098687 ATM/BRCA2/PCNA/CDK1/XRCC1/ERCC1/MSH2     7
## GO:0070522                          XRCC1/ERCC1     2
## GO:0000109                          XRCC1/ERCC1     2
## GO:1990391                            ATM/BRCA2     2
## GO:0042470                      FASN/PRDX1/TFRC     3
##                    ID                              Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding      7/22
## GO:0051434 GO:0051434                       BH3 domain binding      2/22
## GO:0031625 GO:0031625         ubiquitin protein ligase binding      5/22
## GO:0120283 GO:0120283  protein serine/threonine kinase binding      2/22
## GO:0044389 GO:0044389    ubiquitin-like protein ligase binding      5/22
## GO:0051400 GO:0051400                        BH domain binding      2/22
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0140297 478/18522 8.892664e-07 0.0001458397 5.616419e-05
## GO:0051434   6/18522 2.014327e-05 0.0010740097 4.136109e-04
## GO:0031625 305/18522 2.451473e-05 0.0010740097 4.136109e-04
## GO:0120283   7/18522 2.818027e-05 0.0010740097 4.136109e-04
## GO:0044389 324/18522 3.274420e-05 0.0010740097 4.136109e-04
## GO:0051400   9/18522 4.823953e-05 0.0013185470 5.077845e-04
##                                          geneID Count
## GO:0140297 BCL2/MYC/RB1/ETS1/ARID1A/YWHAZ/NCOA3     7
## GO:0051434                          BCL2/BCL2L1     2
## GO:0031625            BCL2/RB1/BID/YWHAZ/CDKN1A     5
## GO:0120283                           XIAP/MAPK8     2
## GO:0044389            BCL2/RB1/BID/YWHAZ/CDKN1A     5
## GO:0051400                          BCL2/BCL2L1     2
##                    ID                                         Description
## GO:0000082 GO:0000082               G1/S transition of mitotic cell cycle
## GO:0044843 GO:0044843                    cell cycle G1/S phase transition
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:1902806 GO:1902806      regulation of cell cycle G1/S phase transition
## GO:0009314 GO:0009314                               response to radiation
## GO:0051402 GO:0051402                            neuron apoptotic process
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0000082     10/22 234/18888 3.988594e-14 7.195423e-11 2.594685e-11
## GO:0044843     10/22 262/18888 1.240888e-13 1.119281e-10 4.036150e-11
## GO:2000045      9/22 185/18888 3.041079e-13 1.828702e-10 6.594340e-11
## GO:1902806      9/22 211/18888 1.001594e-12 4.517189e-10 1.628908e-10
## GO:0009314     10/22 431/18888 1.746889e-11 5.593618e-09 2.017071e-09
## GO:0051402      9/22 292/18888 1.860405e-11 5.593618e-09 2.017071e-09
##                                                           geneID Count
## GO:0000082    BCL2/MYC/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A    10
## GO:0044843    BCL2/MYC/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A    10
## GO:2000045        BCL2/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A     9
## GO:1902806        BCL2/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A     9
## GO:0009314 AKT2/BCL2/MYC/AKT1/BCL2L1/MAPK8/KRAS/ATM/CCND1/CDKN1A    10
## GO:0051402          AKT2/BCL2/BCL2L1/RB1/XIAP/BID/KRAS/ATM/CCND1     9
##                    ID                                        Description
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0097136 GO:0097136                       Bcl-2 family protein complex
## GO:0005741 GO:0005741                       mitochondrial outer membrane
## GO:0031968 GO:0031968                           organelle outer membrane
## GO:0019867 GO:0019867                                     outer membrane
## GO:1902554 GO:1902554            serine/threonine protein kinase complex
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0000307      3/22  56/19894 3.132362e-05 0.002612600 0.001402554
## GO:0097136      2/22  10/19894 5.225199e-05 0.002612600 0.001402554
## GO:0005741      4/22 219/19894 8.944687e-05 0.002980535 0.001600077
## GO:0031968      4/22 248/19894 1.444963e-04 0.002980535 0.001600077
## GO:0019867      4/22 250/19894 1.490267e-04 0.002980535 0.001600077
## GO:1902554      3/22 136/19894 4.375468e-04 0.007119710 0.003822160
##                          geneID Count
## GO:0000307     RB1/CCND1/CDKN1A     3
## GO:0097136          BCL2/BCL2L1     2
## GO:0005741 BCL2/BCL2L1/BID/KRAS     4
## GO:0031968 BCL2/BCL2L1/BID/KRAS     4
## GO:0019867 BCL2/BCL2L1/BID/KRAS     4
## GO:1902554     RB1/CCND1/CDKN1A     3
##                    ID                                        Description
## GO:0004674 GO:0004674           protein serine/threonine kinase activity
## GO:0030544 GO:0030544                              Hsp70 protein binding
## GO:0000014 GO:0000014 single-stranded DNA endodeoxyribonuclease activity
## GO:0003684 GO:0003684                                damaged DNA binding
## GO:0001618 GO:0001618                            virus receptor activity
## GO:0140272 GO:0140272                          exogenous protein binding
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0004674      6/28 427/18522 3.549931e-05 0.007334157 0.003488610
## GO:0030544      3/28  51/18522 6.137370e-05 0.007334157 0.003488610
## GO:0000014      2/28  11/18522 1.201914e-04 0.009366260 0.004455213
## GO:0003684      3/28  73/18522 1.792650e-04 0.009366260 0.004455213
## GO:0001618      3/28  79/18522 2.265476e-04 0.009366260 0.004455213
## GO:0140272      3/28  80/18522 2.351362e-04 0.009366260 0.004455213
##                                      geneID Count
## GO:0004674 MAPK9/EGFR/ACVRL1/EEF2K/ATM/CDK1     6
## GO:0030544                   TSC1/CDK1/TFRC     3
## GO:0000014                      RAD50/ERCC1     2
## GO:0003684                 PARP1/MSH6/ERCC1     3
## GO:0001618                   EGFR/CDK1/TFRC     3
## GO:0140272                   EGFR/CDK1/TFRC     3
##                    ID                                  Description GeneRatio
## GO:0045931 GO:0045931    positive regulation of mitotic cell cycle      6/28
## GO:0051053 GO:0051053 negative regulation of DNA metabolic process      6/28
## GO:0006260 GO:0006260                              DNA replication      7/28
## GO:1904354 GO:1904354      negative regulation of telomere capping      3/28
## GO:0051054 GO:0051054 positive regulation of DNA metabolic process      7/28
## GO:0032205 GO:0032205  negative regulation of telomere maintenance      4/28
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0045931 130/18888 3.149240e-08 4.756438e-05 2.489340e-05
## GO:0051053 142/18888 5.338315e-08 4.756438e-05 2.489340e-05
## GO:0006260 278/18888 1.260997e-07 6.540340e-05 3.422967e-05
## GO:1904354   8/18888 1.625688e-07 6.540340e-05 3.422967e-05
## GO:0051054 301/18888 2.163214e-07 6.540340e-05 3.422967e-05
## GO:0032205  36/18888 2.202135e-07 6.540340e-05 3.422967e-05
##                                             geneID Count
## GO:0045931    EIF4EBP1/EGFR/RAB11A/ASNS/BRCA2/CDK1     6
## GO:0051053         RAD50/PARP1/ATM/TTF1/MSH6/ERCC1     6
## GO:0006260 EGFR/ACVRL1/RAD50/PARP1/BRCA2/TTF1/CDK1     7
## GO:1904354                         RAD50/ATM/ERCC1     3
## GO:0051054    EGFR/RAD50/PARP1/ATM/CDK1/ERCC1/TFRC     7
## GO:0032205                   RAD50/PARP1/ATM/ERCC1     4
##                    ID                  Description GeneRatio   BgRatio
## GO:0000781 GO:0000781 chromosome, telomeric region      6/28 173/19894
## GO:0098687 GO:0098687           chromosomal region      6/28 402/19894
## GO:1990391 GO:1990391           DNA repair complex      2/28  22/19894
## GO:0032301 GO:0032301            MutSalpha complex      1/28   2/19894
## GO:0070435 GO:0070435             Shc-EGFR complex      1/28   2/19894
## GO:0097122 GO:0097122       cyclin A2-CDK1 complex      1/28   2/19894
##                  pvalue     p.adjust       qvalue
## GO:0000781 1.274426e-07 1.771452e-05 9.658807e-06
## GO:0098687 1.695149e-05 1.178128e-03 6.423722e-04
## GO:1990391 4.336552e-04 2.009269e-02 1.095550e-02
## GO:0032301 2.813009e-03 3.994050e-02 2.177748e-02
## GO:0070435 2.813009e-03 3.994050e-02 2.177748e-02
## GO:0097122 2.813009e-03 3.994050e-02 2.177748e-02
##                                      geneID Count
## GO:0000781 RAD50/PARP1/ATM/BRCA2/CDK1/ERCC1     6
## GO:0098687 RAD50/PARP1/ATM/BRCA2/CDK1/ERCC1     6
## GO:1990391                        ATM/BRCA2     2
## GO:0032301                             MSH6     1
## GO:0070435                             EGFR     1
## GO:0097122                             CDK1     1
##                    ID
## GO:1990599 GO:1990599
## GO:0051219 GO:0051219
## GO:0045296 GO:0045296
## GO:0032356 GO:0032356
## GO:0045309 GO:0045309
## GO:0000014 GO:0000014
##                                                               Description
## GO:1990599 3' overhang single-stranded DNA endodeoxyribonuclease activity
## GO:0051219                                         phosphoprotein binding
## GO:0045296                                               cadherin binding
## GO:0032356                                           oxidized DNA binding
## GO:0045309                      protein phosphorylated amino acid binding
## GO:0000014             single-stranded DNA endodeoxyribonuclease activity
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:1990599      2/34   3/18522 9.800794e-06 0.002261592 0.001165410
## GO:0051219      4/34  93/18522 2.461113e-05 0.002261592 0.001165410
## GO:0045296      6/34 333/18522 2.838819e-05 0.002261592 0.001165410
## GO:0032356      2/34  10/18522 1.458311e-04 0.006452867 0.003325195
## GO:0045309      3/34  59/18522 1.712518e-04 0.006452867 0.003325195
## GO:0000014      2/34  11/18522 1.780328e-04 0.006452867 0.003325195
##                                     geneID Count
## GO:1990599                     XRCC1/ERCC1     2
## GO:0051219            SRC/MAPK1/YWHAE/IRS1     4
## GO:0045296 SRC/VASP/YWHAE/ANLN/RAB11B/EGFR     6
## GO:0032356                      XRCC1/MSH6     2
## GO:0045309                MAPK1/YWHAE/IRS1     3
## GO:0000014                     XRCC1/ERCC1     2
##                    ID                                             Description
## GO:0002520 GO:0002520                               immune system development
## GO:0031667 GO:0031667                             response to nutrient levels
## GO:0031929 GO:0031929                                           TOR signaling
## GO:0035051 GO:0035051                              cardiocyte differentiation
## GO:2000641 GO:2000641 regulation of early endosome to late endosome transport
## GO:0038128 GO:0038128                                 ERBB2 signaling pathway
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0002520      8/34 197/18888 1.748005e-09 4.006428e-06 1.943046e-06
## GO:0031667     10/34 490/18888 9.448596e-09 8.637050e-06 4.188815e-06
## GO:0031929      7/34 165/18888 1.507339e-08 8.637050e-06 4.188815e-06
## GO:0035051      7/34 165/18888 1.507339e-08 8.637050e-06 4.188815e-06
## GO:2000641      4/34  19/18888 3.326583e-08 1.524906e-05 7.395519e-06
## GO:0038128      4/34  23/18888 7.561261e-08 2.888402e-05 1.400823e-05
##                                                         geneID Count
## GO:0002520        MAPK1/MAP2K1/ERCC1/RBM15/GATA3/ATM/MSH6/TFRC     8
## GO:0031667 SRC/MAPK1/ITGA2/TSC1/ERCC1/G6PD/ASNS/EGFR/XBP1/TFRC    10
## GO:0031929                 AKT1S1/SRC/TSC1/GSK3A/GATA3/ATM/VHL     7
## GO:0035051              MAPK1/TSC1/PDCD4/GSK3A/G6PD/EGFR/MYH11     7
## GO:2000641                                SRC/MAPK1/MAP2K1/NF2     4
## GO:0038128                               SRC/MAPK1/MAP2K1/EGFR     4
##                    ID                        Description GeneRatio   BgRatio
## GO:0005925 GO:0005925                     focal adhesion      7/34 421/19894
## GO:0030055 GO:0030055            cell-substrate junction      7/34 431/19894
## GO:0070522 GO:0070522                ERCC4-ERCC1 complex      2/34   4/19894
## GO:0000109 GO:0000109 nucleotide-excision repair complex      2/34  12/19894
## GO:0031256 GO:0031256              leading edge membrane      4/34 179/19894
## GO:0005901 GO:0005901                            caveola      3/34  82/19894
##                  pvalue     p.adjust       qvalue
## GO:0005925 5.936393e-06 0.0005571557 0.0002804903
## GO:0030055 6.921189e-06 0.0005571557 0.0002804903
## GO:0070522 1.697422e-05 0.0009109496 0.0004586016
## GO:0000109 1.851213e-04 0.0074511307 0.0037511413
## GO:0031256 2.380182e-04 0.0076641868 0.0038584007
## GO:0005901 3.683101e-04 0.0098070624 0.0049371939
##                                            geneID Count
## GO:0005925 SRC/MAPK1/VASP/ITGA2/YWHAE/MAP2K1/EGFR     7
## GO:0030055 SRC/MAPK1/VASP/ITGA2/YWHAE/MAP2K1/EGFR     7
## GO:0070522                            XRCC1/ERCC1     2
## GO:0000109                            XRCC1/ERCC1     2
## GO:0031256                      SRC/VASP/EGFR/NF2     4
## GO:0005901                         SRC/MAPK1/IRS1     3
##                    ID
## GO:0044389 GO:0044389
## GO:0030331 GO:0030331
## GO:0019887 GO:0019887
## GO:0016538 GO:0016538
## GO:0019207 GO:0019207
## GO:0045294 GO:0045294
##                                                                    Description
## GO:0044389                               ubiquitin-like protein ligase binding
## GO:0030331                                   nuclear estrogen receptor binding
## GO:0019887                                   protein kinase regulator activity
## GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
## GO:0019207                                           kinase regulator activity
## GO:0045294                                               alpha-catenin binding
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0044389      6/34 324/18522 2.433845e-05 0.004948358 0.002443633
## GO:0030331      3/34  39/18522 4.936524e-05 0.004948358 0.002443633
## GO:0019887      5/34 232/18522 6.109083e-05 0.004948358 0.002443633
## GO:0016538      3/34  50/18522 1.044209e-04 0.005906158 0.002916621
## GO:0019207      5/34 270/18522 1.248624e-04 0.005906158 0.002916621
## GO:0045294      2/34  10/18522 1.458311e-04 0.005906158 0.002916621
##                                           geneID Count
## GO:0044389 ERBB3/BECN1/CTNNB1/CCNB1/TUBA1B/PARP1     6
## GO:0030331                     PCNA/CTNNB1/PARP1     3
## GO:0019887        ERBB3/CCNB1/CCNE2/RPTOR/CDKN2A     5
## GO:0016538                    CCNB1/CCNE2/CDKN2A     3
## GO:0019207        ERBB3/CCNB1/CCNE2/RPTOR/CDKN2A     5
## GO:0045294                           CDH2/CTNNB1     2
##                    ID                               Description GeneRatio
## GO:0009410 GO:0009410           response to xenobiotic stimulus     11/34
## GO:1901987 GO:1901987 regulation of cell cycle phase transition     11/34
## GO:0032200 GO:0032200                     telomere organization      8/34
## GO:0000723 GO:0000723                      telomere maintenance      7/34
## GO:0045786 GO:0045786         negative regulation of cell cycle      9/34
## GO:0044772 GO:0044772       mitotic cell cycle phase transition      9/34
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0009410 444/18888 1.882340e-10 2.541885e-07 1.224154e-07
## GO:1901987 455/18888 2.440600e-10 2.541885e-07 1.224154e-07
## GO:0032200 189/18888 1.259232e-09 8.743266e-07 4.210694e-07
## GO:0000723 158/18888 1.116164e-08 5.812427e-06 2.799223e-06
## GO:0045786 405/18888 2.861415e-08 1.192066e-05 5.740903e-06
## GO:0044772 451/18888 7.192558e-08 2.497016e-05 1.202545e-05
##                                                                     geneID
## GO:0009410 BECN1/ITGA2/PCNA/CTNNB1/ACACB/CDK1/E2F1/XRCC1/TYMS/ERRFI1/RPTOR
## GO:1901987 MAPK14/RAD51/BRCA2/ANLN/CDK1/E2F1/CCNB1/EZH2/CCNE2/RPTOR/CDKN2A
## GO:0032200                  RAD51/BRCA2/PCNA/CTNNB1/XRCC1/EZH2/CCNE2/PARP1
## GO:0000723                       RAD51/BRCA2/PCNA/CTNNB1/XRCC1/CCNE2/PARP1
## GO:0045786           MAPK14/RAD51/BRCA2/CTNNB1/CDK1/E2F1/CCNB1/EZH2/CDKN2A
## GO:0044772              ANLN/CDK1/E2F1/CCNB1/FOXM1/EZH2/CCNE2/RPTOR/CDKN2A
##            Count
## GO:0009410    11
## GO:1901987    11
## GO:0032200     8
## GO:0000723     7
## GO:0045786     9
## GO:0044772     9
##                    ID                                        Description
## GO:0000781 GO:0000781                       chromosome, telomeric region
## GO:0098687 GO:0098687                                 chromosomal region
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0097125 GO:0097125                             cyclin B1-CDK1 complex
## GO:1902554 GO:1902554            serine/threonine protein kinase complex
## GO:0005916 GO:0005916                                    fascia adherens
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0000781      7/34 173/19894 1.469642e-08 2.792320e-06 1.392293e-06
## GO:0098687      8/34 402/19894 2.972081e-07 2.823477e-05 1.407828e-05
## GO:0000307      4/34  56/19894 2.451862e-06 1.346679e-04 6.714743e-05
## GO:0097125      2/34   2/19894 2.835114e-06 1.346679e-04 6.714743e-05
## GO:1902554      4/34 136/19894 8.264048e-05 3.140338e-03 1.565820e-03
## GO:0005916      2/34   9/19894 1.013006e-04 3.207851e-03 1.599482e-03
##                                                  geneID Count
## GO:0000781       RAD51/BRCA2/PCNA/CDK1/XRCC1/EZH2/PARP1     7
## GO:0098687 RAD51/BRCA2/PCNA/CDK1/XRCC1/CCNB1/EZH2/PARP1     8
## GO:0000307                        PCNA/CDK1/CCNB1/CCNE2     4
## GO:0097125                                   CDK1/CCNB1     2
## GO:1902554                        PCNA/CDK1/CCNB1/CCNE2     4
## GO:0005916                                  CDH2/CTNNB1     2
##                    ID                                            Description
## GO:0045309 GO:0045309              protein phosphorylated amino acid binding
## GO:0051219 GO:0051219                                 phosphoprotein binding
## GO:0043125 GO:0043125                          ErbB-3 class receptor binding
## GO:0042169 GO:0042169                                     SH2 domain binding
## GO:0004715 GO:0004715 non-membrane spanning protein tyrosine kinase activity
## GO:0001784 GO:0001784                        phosphotyrosine residue binding
##            GeneRatio  BgRatio       pvalue     p.adjust       qvalue
## GO:0045309      4/35 59/18522 4.515759e-06 0.0009257306 0.0005038637
## GO:0051219      4/35 93/18522 2.768030e-05 0.0023619941 0.0012856040
## GO:0043125      2/35  5/18522 3.456577e-05 0.0023619941 0.0012856040
## GO:0042169      3/35 42/18522 6.746261e-05 0.0032346697 0.0017605904
## GO:0004715      3/35 45/18522 8.306481e-05 0.0032346697 0.0017605904
## GO:0001784      3/35 47/18522 9.467326e-05 0.0032346697 0.0017605904
##                         geneID Count
## GO:0045309 MAPK1/LCK/YWHAB/SYK     4
## GO:0051219 MAPK1/LCK/YWHAB/SYK     4
## GO:0043125          ERBB3/NRG1     2
## GO:0042169        PTK2/LCK/SYK     3
## GO:0004715        PTK2/LCK/SYK     3
## GO:0001784       MAPK1/LCK/SYK     3
##                    ID                                       Description
## GO:0051402 GO:0051402                          neuron apoptotic process
## GO:0002757 GO:0002757      immune response-activating signaling pathway
## GO:0038133 GO:0038133                     ERBB2-ERBB3 signaling pathway
## GO:0038129 GO:0038129                           ERBB3 signaling pathway
## GO:0043254 GO:0043254 regulation of protein-containing complex assembly
## GO:0071383 GO:0071383     cellular response to steroid hormone stimulus
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0051402      8/36 292/18888 6.161328e-08 0.0001262456 0.0000676449
## GO:0002757      9/36 500/18888 2.959587e-07 0.0003032097 0.0001624658
## GO:0038133      3/36   9/18888 5.299354e-07 0.0003619459 0.0001939378
## GO:0038129      3/36  10/18888 7.560587e-07 0.0003872911 0.0002075182
## GO:0043254      8/36 418/18888 9.458263e-07 0.0003875996 0.0002076835
## GO:0071383      6/36 213/18888 2.814942e-06 0.0009613026 0.0005150850
##                                                     geneID Count
## GO:0051402       ERBB3/AKT2/GATA3/AXL/TP63/BID/PARP1/CASP9     8
## GO:0002757 ESR1/GATA3/MAPK1/BIRC2/PTK2/MS4A1/LCK/PARP1/SYK     9
## GO:0038133                                ERBB3/MAPK1/NRG1     3
## GO:0038129                                ERBB3/MAPK1/NRG1     3
## GO:0043254      CLDN7/EIF4G1/BIRC2/PRRT2/NRG1/BID/TFRC/SYK     8
## GO:0071383              ESR1/MAPK1/TP63/ERRFI1/PARP1/CASP9     6
##                    ID             Description GeneRatio   BgRatio       pvalue
## GO:0031143 GO:0031143            pseudopodium      2/36  18/19894 0.0004783253
## GO:0005925 GO:0005925          focal adhesion      5/36 421/19894 0.0009099010
## GO:0030055 GO:0030055 cell-substrate junction      5/36 431/19894 0.0010105551
## GO:0044853 GO:0044853    plasma membrane raft      3/36 113/19894 0.0011114266
## GO:0016342 GO:0016342         catenin complex      2/36  31/19894 0.0014323951
## GO:0045121 GO:0045121           membrane raft      4/36 286/19894 0.0017151002
##             p.adjust     qvalue                       geneID Count
## GO:0031143 0.0429315 0.02638322                  MAPK1/RAB25     2
## GO:0005925 0.0429315 0.02638322 MAPK1/PTK2/CTNNA1/MYH9/YWHAB     5
## GO:0030055 0.0429315 0.02638322 MAPK1/PTK2/CTNNA1/MYH9/YWHAB     5
## GO:0044853 0.0429315 0.02638322           MAPK1/MS4A1/CTNNA1     3
## GO:0016342 0.0429315 0.02638322                  CDH3/CTNNA1     2
## GO:0045121 0.0429315 0.02638322       MAPK1/MS4A1/LCK/CTNNA1     4
##                    ID                           Description GeneRatio   BgRatio
## GO:0045296 GO:0045296                      cadherin binding     10/44 333/18522
## GO:0031625 GO:0031625      ubiquitin protein ligase binding      8/44 305/18522
## GO:0042826 GO:0042826           histone deacetylase binding      6/44 128/18522
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding      8/44 324/18522
## GO:0050815 GO:0050815         phosphoserine residue binding      3/44  10/18522
## GO:0008013 GO:0008013                  beta-catenin binding      5/44  86/18522
##                  pvalue     p.adjust       qvalue
## GO:0045296 4.449265e-09 1.299185e-06 6.509977e-07
## GO:0031625 5.222688e-07 5.364286e-05 2.687944e-05
## GO:0042826 5.511253e-07 5.364286e-05 2.687944e-05
## GO:0044389 8.238420e-07 6.014046e-05 3.013527e-05
## GO:0050815 1.483568e-06 8.664034e-05 4.341387e-05
## GO:0008013 1.806890e-06 8.793532e-05 4.406276e-05
##                                                              geneID Count
## GO:0045296 CDH1/YWHAZ/YWHAE/NDRG1/FASN/MYH9/CTNNA1/EEF2/PRDX1/YWHAB    10
## GO:0031625        TUBA1B/YWHAZ/YWHAE/TP53/CDKN1A/CDKN1B/PARP1/GSK3B     8
## GO:0042826                       MAPK8/YWHAE/TP53/CCND1/PARP1/YWHAB     6
## GO:0044389        TUBA1B/YWHAZ/YWHAE/TP53/CDKN1A/CDKN1B/PARP1/GSK3B     8
## GO:0050815                                        YWHAZ/YWHAE/YWHAB     3
## GO:0008013                                 CDH1/AR/CTNNA1/GSK3B/PXN     5
##                    ID
## GO:0034504 GO:0034504
## GO:1900180 GO:1900180
## GO:0031334 GO:0031334
## GO:0045936 GO:0045936
## GO:0010563 GO:0010563
## GO:0062197 GO:0062197
##                                                           Description GeneRatio
## GO:0034504                            protein localization to nucleus     12/44
## GO:1900180              regulation of protein localization to nucleus      9/44
## GO:0031334 positive regulation of protein-containing complex assembly      9/44
## GO:0045936         negative regulation of phosphate metabolic process     11/44
## GO:0010563        negative regulation of phosphorus metabolic process     11/44
## GO:0062197                       cellular response to chemical stress     10/44
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0034504 311/18888 4.232578e-12 1.086079e-08 5.243941e-09
## GO:1900180 144/18888 3.820625e-11 4.901862e-08 2.366777e-08
## GO:0031334 197/18888 6.290483e-10 3.995743e-07 1.929273e-07
## GO:0045936 378/18888 7.572262e-10 3.995743e-07 1.929273e-07
## GO:0010563 379/18888 7.785937e-10 3.995743e-07 1.929273e-07
## GO:0062197 311/18888 1.917069e-09 8.198664e-07 3.958579e-07
##                                                                         geneID
## GO:0034504 CDH1/YWHAZ/YWHAE/TP53/CDKN1A/NF2/PARP1/CTNNA1/MTOR/GSK3B/TFRC/WWTR1
## GO:1900180                   CDH1/YWHAZ/NF2/PARP1/CTNNA1/MTOR/GSK3B/TFRC/WWTR1
## GO:0031334                ATM/MAPK8/EIF4G1/TP53/CDKN1B/BCL2L11/MTOR/GSK3B/TFRC
## GO:0045936    EIF4G1/YWHAE/TP53/CDKN1A/NF2/ADAR/CDKN1B/PARP1/GSK3B/WWTR1/YWHAB
## GO:0010563    EIF4G1/YWHAE/TP53/CDKN1A/NF2/ADAR/CDKN1B/PARP1/GSK3B/WWTR1/YWHAB
## GO:0062197              CASP3/ATM/MAPK8/TP53/MAPK1/PARP1/MTOR/PRDX1/PRKAA1/PXN
##            Count
## GO:0034504    12
## GO:1900180     9
## GO:0031334     9
## GO:0045936    11
## GO:0010563    11
## GO:0062197    10
##                    ID             Description GeneRatio   BgRatio       pvalue
## GO:0042470 GO:0042470              melanosome      6/44 112/19894 1.649743e-07
## GO:0048770 GO:0048770         pigment granule      6/44 112/19894 1.649743e-07
## GO:0005901 GO:0005901                 caveola      4/44  82/19894 3.210058e-05
## GO:0005925 GO:0005925          focal adhesion      7/44 421/19894 3.524035e-05
## GO:0030055 GO:0030055 cell-substrate junction      7/44 431/19894 4.090619e-05
## GO:0005912 GO:0005912       adherens junction      5/44 188/19894 5.754759e-05
##                p.adjust       qvalue                                  geneID
## GO:0042470 1.657992e-05 1.024577e-05       YWHAZ/YWHAE/FASN/PRDX1/TFRC/YWHAB
## GO:0048770 1.657992e-05 1.024577e-05       YWHAZ/YWHAE/FASN/PRDX1/TFRC/YWHAB
## GO:0005901 1.644429e-03 1.016196e-03                 CDH1/MAPK1/CTNNA1/IGF1R
## GO:0005925 1.644429e-03 1.016196e-03 YWHAZ/YWHAE/MAPK1/MYH9/CTNNA1/PXN/YWHAB
## GO:0030055 1.644429e-03 1.016196e-03 YWHAZ/YWHAE/MAPK1/MYH9/CTNNA1/PXN/YWHAB
## GO:0005912 1.927844e-03 1.191336e-03              CDH1/NDRG1/NF2/MYH9/CTNNA1
##            Count
## GO:0042470     6
## GO:0048770     6
## GO:0005901     4
## GO:0005925     7
## GO:0030055     7
## GO:0005912     5
##                    ID                              Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity     15/71
## GO:0106310 GO:0106310           protein serine kinase activity     14/71
## GO:0019902 GO:0019902                      phosphatase binding     10/71
## GO:0019903 GO:0019903              protein phosphatase binding      9/71
## GO:0043548 GO:0043548    phosphatidylinositol 3-kinase binding      5/71
## GO:0019207 GO:0019207                kinase regulator activity     10/71
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0004674 427/18522 6.087015e-11 1.679792e-08 7.710955e-09
## GO:0106310 363/18522 8.420009e-11 1.679792e-08 7.710955e-09
## GO:0019902 189/18522 2.595931e-09 3.452588e-07 1.584884e-07
## GO:0019903 142/18522 3.526298e-09 3.517482e-07 1.614673e-07
## GO:0043548  25/18522 3.590014e-08 2.864831e-06 1.315079e-06
## GO:0019207 270/18522 7.747783e-08 5.152276e-06 2.365113e-06
##                                                                                              geneID
## GO:0004674 CDK1/RPS6KB1/MAPK14/EGFR/ARAF/MAPK9/AKT2/MAP2K1/AKT3/GSK3B/PRKAA1/PRKCA/MAPK3/MAPK8/BRAF
## GO:0106310      CDK1/RPS6KB1/MAPK14/ARAF/MAPK9/AKT2/MAP2K1/AKT3/GSK3B/PRKAA1/PRKCA/MAPK3/MAPK8/BRAF
## GO:0019902                            PIK3R1/RPS6KB1/MAPK14/EGFR/PIK3R2/TP53/CTNNB1/MAPK3/MAPK8/PXN
## GO:0019903                                  PIK3R1/RPS6KB1/MAPK14/EGFR/PIK3R2/TP53/CTNNB1/MAPK8/PXN
## GO:0043548                                                           PIK3R1/IRS1/PIK3R2/IGF1R/BECN1
## GO:0019207                            CCNE1/CAV1/PIK3R1/CCND1/CDKN1A/EGFR/PIK3R2/MAP2K1/CCNB1/YWHAB
##            Count
## GO:0004674    15
## GO:0106310    14
## GO:0019902    10
## GO:0019903     9
## GO:0043548     5
## GO:0019207    10
##                    ID                                 Description GeneRatio
## GO:0018105 GO:0018105             peptidyl-serine phosphorylation     18/72
## GO:0018209 GO:0018209                peptidyl-serine modification     18/72
## GO:0048732 GO:0048732                           gland development     20/72
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     18/72
## GO:0104004 GO:0104004 cellular response to environmental stimulus     18/72
## GO:0009410 GO:0009410             response to xenobiotic stimulus     19/72
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0018105 282/18888 1.586060e-17 5.592449e-14 2.502636e-14
## GO:0018209 294/18888 3.325078e-17 5.862112e-14 2.623311e-14
## GO:0048732 449/18888 2.182362e-16 2.226695e-13 9.964523e-14
## GO:0071214 334/18888 3.157537e-16 2.226695e-13 9.964523e-14
## GO:0104004 334/18888 3.157537e-16 2.226695e-13 9.964523e-14
## GO:0009410 444/18888 2.885601e-15 1.695771e-12 7.588623e-13
##                                                                                                                      geneID
## GO:0018105          PTEN/CAV1/CDK1/RPS6KB1/MAPK14/EGFR/ARAF/MAPK9/PTGS2/AKT2/AKT3/EIF4G1/GSK3B/PRKAA1/PRKCA/MAPK8/TFRC/BRAF
## GO:0018209          PTEN/CAV1/CDK1/RPS6KB1/MAPK14/EGFR/ARAF/MAPK9/PTGS2/AKT2/AKT3/EIF4G1/GSK3B/PRKAA1/PRKCA/MAPK8/TFRC/BRAF
## GO:0048732 CAV1/ITGA2/SRSF1/CCND1/EGFR/TP63/EZH2/BRCA2/TYMS/AKT2/MAP2K1/NFKB1/ERRFI1/CTNNB1/SMAD4/PCNA/MAPK3/TGM2/FASN/BRAF
## GO:0071214         PTEN/PIK3R1/ITGA2/RAD51/MAPK14/CDKN1A/MYC/EGFR/BRCA2/PTGS2/TP53/AKT2/NFKB1/IGF1R/PCNA/MAPK3/MAPK8/RAB11B
## GO:0104004         PTEN/PIK3R1/ITGA2/RAD51/MAPK14/CDKN1A/MYC/EGFR/BRCA2/PTGS2/TP53/AKT2/NFKB1/IGF1R/PCNA/MAPK3/MAPK8/RAB11B
## GO:0009410   CDK1/ITGA2/RPS6KB1/E2F1/CCND1/CDKN1A/MYC/EGFR/PTGS2/TYMS/TP53/ERRFI1/CTNNB1/IGFBP2/PCNA/PRKAA1/TFRC/BECN1/BRAF
##            Count
## GO:0018105    18
## GO:0018209    18
## GO:0048732    20
## GO:0071214    18
## GO:0104004    18
## GO:0009410    19
##                    ID
## GO:0061695 GO:0061695
## GO:1902911 GO:1902911
## GO:0005901 GO:0005901
## GO:0005925 GO:0005925
## GO:0030055 GO:0030055
## GO:0000307 GO:0000307
##                                                               Description
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:1902911                                         protein kinase complex
## GO:0005901                                                        caveola
## GO:0005925                                                 focal adhesion
## GO:0030055                                        cell-substrate junction
## GO:0000307             cyclin-dependent protein kinase holoenzyme complex
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0061695     12/72 308/19894 1.026747e-09 3.172649e-07 1.653604e-07
## GO:1902911      9/72 150/19894 3.513936e-09 5.429032e-07 2.829643e-07
## GO:0005901      7/72  82/19894 1.848300e-08 1.903749e-06 9.922452e-07
## GO:0005925     12/72 421/19894 3.368808e-08 2.602404e-06 1.356389e-06
## GO:0030055     12/72 431/19894 4.356805e-08 2.633625e-06 1.372661e-06
## GO:0000307      6/72  56/19894 5.113836e-08 2.633625e-06 1.372661e-06
##                                                                              geneID
## GO:0061695 CCNE1/PIK3R1/CDK1/CCND1/CDKN1A/IRS1/PIK3R2/CCNB1/IGF1R/PCNA/PRKAA1/BECN1
## GO:1902911                     CCNE1/CDK1/CCND1/CDKN1A/IRS1/CCNB1/IGF1R/PCNA/PRKAA1
## GO:0005901                                CAV1/IRS1/PTGS2/CTNNA1/CTNNB1/IGF1R/MAPK3
## GO:0005925    CAV1/ITGA2/MYH9/EGFR/PIK3R2/MAP2K1/CTNNA1/CTNNB1/MAPK3/PXN/TGM2/YWHAB
## GO:0030055    CAV1/ITGA2/MYH9/EGFR/PIK3R2/MAP2K1/CTNNA1/CTNNB1/MAPK3/PXN/TGM2/YWHAB
## GO:0000307                                       CCNE1/CDK1/CCND1/CDKN1A/CCNB1/PCNA
##            Count
## GO:0061695    12
## GO:1902911     9
## GO:0005901     7
## GO:0005925    12
## GO:0030055    12
## GO:0000307     6
barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, Factor 1 of 1")

barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, Factor 1 of 2")

barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, Factor 2 of 2")

barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, Factor 1 of 3")

barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, Factor 2 of 3")

barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, Factor 3 of 3")

barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, Factor 1 of 5")

barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, Factor 2 of 5")

barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, Factor 3 of 5")

barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, Factor 4 of 5")

barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, Factor 5 of 5")

barplot(ego_MF[[12]], title = "enrichGO, Molecular Function, Factor 1 of 10")

barplot(ego_MF[[13]], title = "enrichGO, Molecular Function, Factor 2 of 10")

barplot(ego_MF[[14]], title = "enrichGO, Molecular Function, Factor 3 of 10")

barplot(ego_MF[[15]], title = "enrichGO, Molecular Function, Factor 4 of 10")

barplot(ego_MF[[16]], title = "enrichGO, Molecular Function, Factor 5 of 10")

barplot(ego_MF[[17]], title = "enrichGO, Molecular Function, Factor 6 of 10")

barplot(ego_MF[[18]], title = "enrichGO, Molecular Function, Factor 7 of 10")

barplot(ego_MF[[19]], title = "enrichGO, Molecular Function, Factor 8 of 10")

barplot(ego_MF[[20]], title = "enrichGO, Molecular Function, Factor 9 of 10")

barplot(ego_MF[[21]], title = "enrichGO, Molecular Function, Factor 10 of 10")

barplot(ego_BP[[1]], title = "enrichGO, Biological Process, Factor 1 of 1")

barplot(ego_BP[[2]], title = "enrichGO, Biological Process, Factor 1 of 2")

barplot(ego_BP[[3]], title = "enrichGO, Biological Process, Factor 2 of 2")

barplot(ego_BP[[4]], title = "enrichGO, Biological Process, Factor 1 of 3")

barplot(ego_BP[[5]], title = "enrichGO, Biological Process, Factor 2 of 3")

barplot(ego_BP[[6]], title = "enrichGO, Biological Process, Factor 3 of 3")

barplot(ego_BP[[7]], title = "enrichGO, Biological Process, Factor 1 of 5")

barplot(ego_BP[[8]], title = "enrichGO, Biological Process, Factor 2 of 5")

barplot(ego_BP[[9]], title = "enrichGO, Biological Process, Factor 3 of 5")

barplot(ego_BP[[10]], title = "enrichGO, Biological Process, Factor 4 of 5")

barplot(ego_BP[[11]], title = "enrichGO, Biological Process, Factor 5 of 5")

barplot(ego_BP[[12]], title = "enrichGO, Biological Process, Factor 1 of 10")

barplot(ego_BP[[13]], title = "enrichGO, Biological Process, Factor 2 of 10")

barplot(ego_BP[[14]], title = "enrichGO, Biological Process, Factor 3 of 10")

barplot(ego_BP[[15]], title = "enrichGO, Biological Process, Factor 4 of 10")

barplot(ego_BP[[16]], title = "enrichGO, Biological Process, Factor 5 of 10")

barplot(ego_BP[[17]], title = "enrichGO, Biological Process, Factor 6 of 10")

barplot(ego_BP[[18]], title = "enrichGO, Biological Process, Factor 7 of 10")

barplot(ego_BP[[19]], title = "enrichGO, Biological Process, Factor 8 of 10")

barplot(ego_BP[[20]], title = "enrichGO, Biological Process, Factor 9 of 10")

barplot(ego_BP[[21]], title = "enrichGO, Biological Process, Factor 10 of 10")

barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, Factor 1 of 1")

barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, Factor 1 of 2")

barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, Factor 2 of 2")

barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, Factor 1 of 3")

barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, Factor 2 of 3")

barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, Factor 3 of 3")

barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, Factor 1 of 5")

barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, Factor 2 of 5")

barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, Factor 3 of 5")

barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, Factor 4 of 5")

barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, Factor 5 of 5")

barplot(ego_CC[[12]], title = "enrichGO, Cellular Component, Factor 1 of 10")

barplot(ego_CC[[13]], title = "enrichGO, Cellular Component, Factor 2 of 10")

barplot(ego_CC[[14]], title = "enrichGO, Cellular Component, Factor 3 of 10")

barplot(ego_CC[[15]], title = "enrichGO, Cellular Component, Factor 4 of 10")

barplot(ego_CC[[16]], title = "enrichGO, Cellular Component, Factor 5 of 10")

barplot(ego_CC[[17]], title = "enrichGO, Cellular Component, Factor 6 of 10")

barplot(ego_CC[[18]], title = "enrichGO, Cellular Component, Factor 7 of 10")

barplot(ego_CC[[19]], title = "enrichGO, Cellular Component, Factor 8 of 10")

barplot(ego_CC[[20]], title = "enrichGO, Cellular Component, Factor 9 of 10")

barplot(ego_CC[[21]], title = "enrichGO, Cellular Component, Factor 10 of 10")

DAG plots for ego

goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 1")

goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 2")

goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 2")

goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 3")

goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 3")

goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, Factor 3 of 3")

goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 5")

goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 5")

goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, Factor 3 of 5")

goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, Factor 4 of 5")

goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, Factor 5 of 5")

goplot(ego_MF[[12]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 10")

goplot(ego_MF[[13]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 10")

goplot(ego_MF[[14]]) + labs(title = "enrichGO, Molecular Function, Factor 3 of 10")

goplot(ego_MF[[15]]) + labs(title = "enrichGO, Molecular Function, Factor 4 of 10")

goplot(ego_MF[[16]]) + labs(title = "enrichGO, Molecular Function, Factor 5 of 10")

goplot(ego_MF[[17]]) + labs(title = "enrichGO, Molecular Function, Factor 6 of 10")

goplot(ego_MF[[18]]) + labs(title = "enrichGO, Molecular Function, Factor 7 of 10")

goplot(ego_MF[[19]]) + labs(title = "enrichGO, Molecular Function, Factor 8 of 10")

goplot(ego_MF[[20]]) + labs(title = "enrichGO, Molecular Function, Factor 9 of 10")

goplot(ego_MF[[21]]) + labs(title = "enrichGO, Molecular Function, Factor 10 of 10")

goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 1")

goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 2")
## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 2")

goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 3")

goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 3")

goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, Factor 3 of 3")
## Warning: ggrepel: 6 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 5")

goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 5")

goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, Factor 3 of 5")

goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, Factor 4 of 5")

goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, Factor 5 of 5")

goplot(ego_BP[[12]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 10")
## Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[13]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 10")

goplot(ego_BP[[14]]) + labs(title = "enrichGO, Biological Process, Factor 3 of 10")
## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[15]]) + labs(title = "enrichGO, Biological Process, Factor 4 of 10")

goplot(ego_BP[[16]]) + labs(title = "enrichGO, Biological Process, Factor 5 of 10")
## Warning: ggrepel: 5 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[17]]) + labs(title = "enrichGO, Biological Process, Factor 6 of 10")
## Warning: ggrepel: 10 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[18]]) + labs(title = "enrichGO, Biological Process, Factor 7 of 10")
## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[19]]) + labs(title = "enrichGO, Biological Process, Factor 8 of 10")

goplot(ego_BP[[20]]) + labs(title = "enrichGO, Biological Process, Factor 9 of 10")

goplot(ego_BP[[21]]) + labs(title = "enrichGO, Biological Process, Factor 10 of 10")

goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 1")

goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 2")

goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 2")

goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 3")

goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 3")

goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, Factor 3 of 3")

goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 5")

goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 5")

goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, Factor 3 of 5")

goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, Factor 4 of 5")

goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, Factor 5 of 5")

goplot(ego_CC[[12]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 10")

goplot(ego_CC[[13]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 10")

goplot(ego_CC[[14]]) + labs(title = "enrichGO, Cellular Component, Factor 3 of 10")

goplot(ego_CC[[15]]) + labs(title = "enrichGO, Cellular Component, Factor 4 of 10")

goplot(ego_CC[[16]]) + labs(title = "enrichGO, Cellular Component, Factor 5 of 10")

goplot(ego_CC[[17]]) + labs(title = "enrichGO, Cellular Component, Factor 6 of 10")

goplot(ego_CC[[18]]) + labs(title = "enrichGO, Cellular Component, Factor 7 of 10")

goplot(ego_CC[[19]]) + labs(title = "enrichGO, Cellular Component, Factor 8 of 10")

goplot(ego_CC[[20]]) + labs(title = "enrichGO, Cellular Component, Factor 9 of 10")

goplot(ego_CC[[21]]) + labs(title = "enrichGO, Cellular Component, Factor 10 of 10")

3. Export Pathway Analysis result to data

pathway = list("ggo_MF" = ggo_MF,
               "ggo_BP" = ggo_BP,
               "ggo_CC" = ggo_CC,
               "ego_MF" = ego_MF,
               "ego_BP" = ego_BP,
               "ego_CC" = ego_CC)

saveRDS(pathway, file = "data/out_pathway/pathways_mofa_top_5_percent.rds")